Always Coming Home: Subverted in one of the creation myths. One world did rise from a brother and sister who were the only ones left from the previous one, but since it was incest, the new people were mad and destroyed themselves eventually.
Animorphs: Played in the The Change. There are several Adam and Eve references to Jara Hamee and Ket Halpak, the first two free Hork-Bajir since the Yeerks enslaved them.
Die Insel Felsenburg: The protagonist and his wife populate an entire desert island.
Evolution: Subverted in "The Long Shadow". The sole female member of the reawakened squadron runs away because she knows the men want to enact this with her.
Homecoming Saga: Sixteen people (only four of whom had no genetic connection to someone else in the group) from the planet Harmony are selected to return to Earth and re-establish the human population. It's established that since the Oversoul (the supercomputer that has been running the planet for millennia) has been running a breeding program for just this situation, any recessive traits that would pop up in such a closed population have been bred out of them (it's also revealed that Harmony is not the only such human-populated planet, nor is it the first to return to Earth).
Le Dernier Homme (The Last Man): Subverts this, set in a far future apocalyptic dying-earth where human fertility has drastically dropped, Omegarus, the son of the king of Europe and also the last child to be born in Europe is encouraged by the spirit of the earth to travel to seek out Syderia, the last fertile woman in Brazil, the pair are often compared to Adam and Eve, they even meet and recount their story to the biblical Adam himself who, while hiding his identity, is sent to convince the pair not to repopulate the human race.
Subverted in "The Silent Towns". A man wakes up to find that he's been left on Mars by accident after most of the Martian colony has gone back to Earth. He begins dialing phone numbers in a desperate attempt for human contact and manages get in touch with a woman, who he begins to fall in love with (based on their brief phone conversation). When they finally meet, he finds her obnoxious and decides he'd prefer a life of isolation.
The final story plays the trope fairly straight though, although it leaves it open whether or not "Adam and Eve" will actually meet up (and the human race will continue).
New Beginning features the protagonists fleeing their doomed homeworld made up entirely of things named in English with one letter shifted to Earth on the Ark. Adam and Eve are two of the children on the Ark, and are sufficiently troublesome that the others leave them on Earth with the cavemen. Not the last of their species, but the other children go into stasis on the ship and wait.
"Not with a Bang", a Damon Knight short story, has two survivors of a biological war, one being an infirm pilot who barely survived the plague and the other being a nurse who had a natural immunity. The repopulating never happens, because she is a very moral woman and they're not married (and where are they going to find a priest?). After much coaxing and cajoling, she agrees to marry him. He then suffers a final attack of the sickness in the one place she would never follow him: the men's bathroom. The story also directly addresses the incest issue — namely, the Adam finds his Eve so annoying he plans to leave her for their first daughter. On the other hand, it never precludes the possibility that more successful Adam and Eve Plots happened.
Orphans of the Sky: Implicitly. At the end, the sole landing party on the new planet consists of Hugh, Bill, Alan, and their wives, who do not have the means to leave once they get there, with the implication being that will serve as the founders of a new human population there. A brief passage in Time Enough for Love indicates that, although the original Generation Ship that they came from was eventually found entirely lifeless due to social decay, the descendants of Hugh's group were found alive on their planet when the ship's course was backtracked.
Subverted in a completely different way by Larry Niven's short story "What Can You Say About Chocolate Coated Manhole Covers?" The story begins with the main characters at a party having a fun conversation. They speculate on how the Adam and Eve legend could work in real life, purely as an intellectual exercise. They conclude, for the obvious reasons, that one pair could not populate an entire planet. They come up with an elaborate scheme based on Real Life stock breeding techniques, involving many pairs and small groups that are isolated from each other by geography. Then... an alien kidnaps the protagonists, strands them on a planet orbiting Alpha Centauri, and tells them that they've just figured out the aliens' secret plan for breeding an 'improved' form of human being.
Parodied in Harlan Ellison's short-short story "The Voice in the Garden". Two humans who are sole survivors of some sort meet each other and decide to do this. The woman is of course named Eve, and the man... George.
In one of Michael Swanwick's "element" short-shorts, an experiment creates a new universe populated by one man and one woman. The man's name is Adam, so naturally the woman takes a new name... Jennifer.
In The Firebringer Trilogy, four hundred years before the books begin, the unicorns' princess and warleader sends four scouts out to seek verification of claims being made by wyverns who want to emigrate to the same territory as the unicorns. Quite some time after the scouts leave, one comes stumbling back with the news the four were sent to get, and notes that one of their companions died along the way. The other two were kept as hostages. Fast-forward four hundred years to the travels of Jan, the books' main character, and when he reaches that part of the world what does he find but a small, well-protected herd of unicorns who all look very much like the descendants of the last two scouts. And yes, the incest factor is acknowledged. There's also the implication that these unicorns wouldn't have survived to breed to these numbers if they hadn't had the protection of powerful dragons.
Subverted in Haruhi Suzumiya. After Haruhi starts splitting off another dimension containing (at the moment) only Kyon and herself, Itsuki temporarily appears from the original world and jokes that Kyon and Haruhi could be the new Adam and Eve and populate the world. Kyon is not amused. Itsuki then theorizes that that won't truly be necessary, and that this new world will become more and more populated as Haruhi continues subconsciously creating it.
Xanth has numerous examples of this trope with novel types of crossbreeds. Typically, it starts with one crossbreed looking for another of his/her kind to mate with. Somehow, he/she finds one, and then a few books later their child goes on a similar quest.
Toyed with the first novel. After doing research in Castle Roogna, Trent is the first person to realize that even though there are plenty of humans around, without fresh blood the omnipresence of magic will eventually lead to humanity's extinction. They will keep producing more crossbreeds, or just plain mutate from too much magic (Humphrey is implied to be on his way to becoming this). As inconvenient as the sporadic invasions from Mundania are, they provide fresh, non-magical genetic stock for humanity.
Eventually subverted in the case of the winged centaurs. When we first meet them, there's just the two of them and this trope seems to be in full force. In later volumes, we find out that they've been gathering volunteers from other races to be transformed by Magician Trent into winged centaurs.
In Jam, when Travis and Tim meet a female survivor Angela, Tim the over-excited survivalist tells Travis to be nice to Angela since they'll eventually have to rebuild the human race with her. Of course, Tim only says this when Angela is out of earshot.
Averted in the Dragonriders of Pern short story "Rescue Run" by the handful of colonists left alive on the Southern Continent of Pern. Convinced that all other humans have been wiped out by Threadfall, domineering jerkass Kimmer forces marriage on the sole remaining female in his group, then refuses to allow any further breeding due to the limited gene pool.
In The Magician's Nephew, Aslan appoints a London cabby and his wife to be Narnia's first king and queen, as well as its first (and only) human inhabitants. Incest issues are averted when their kids grow up to marry wood nymphs and other spirits. This eventually dilutes their bloodline to a point where, when the White Witch returns to conquer Narnia, there's apparently no one left in Narnia who's human enough to contest her claim. After a time, Aslan sends the Pevensie children to do so.
However, Narnia has a sister country in their ally of Archenland, which was fully populated by humans. Also, the subornate island nations, and the southern enemy nation of Calormene. There's not much explanation for how these people got there, though it might have been similar to how the Telmarenes showed up. C. S. Lewis didn't expect to write more than the first book, until popular demand had him go back and expand the world.
According to CS Lewis' official timeline for the history of Narnia, the first humans - as well as intermarrying with Narnian nymphs and dryads and stars and the like - also quickly spread out within a handful of generations to colonise the until-then mostly barren neighbouring lands of Archenland and Calormene. All the part-humans in those three lands could trace their heritage back to the very first humans to enter Narnia (Frank and his wife). The Telmarines, by contrast, were pirates shipwrecked on an island who accidentally crossed over to a land bordering Narnia, established themselves there as the Kingdom of Telmar, and invaded Narnia shortly after the Pevensies left at the end of The Lion, the Witch, and the Wardrobe.
Another classic subversion is "Adam and No Eve" by Alfred Bester, in which the protagonist would be happy to fulfill the plot, but no woman is available. At the end of the story, he drowns himself so that his bacteria will survive in the ocean and hopefully evolve into a new sentient species one day, needing no Adam and no Eve.
The Time Ships: An expedition from an alternative Great Britain becomes stranded in the deep past after an attack from a time-traveling bomber from their enemies in their own time. They survive, and the protagonist gets to watch them rise from a tiny tribe to a space-traveling civilization as he travels in time, a sequence which is rather unpleasantly like watching mold conquer a petri dish.
Z for Zachariah: Anne imagines this with Mr. Loomis since they are, or so she believes, the last survivors in America and possibly the whole world following a nuclear war. Turns out he was way ahead of her, leading to Attempted Rape and causing her to run away from him, which forms the catalyst for the ending of the book.
At one point in Last and First Men, the entire human species reduced to roughly a dozen individuals. They manage to repopulate the Earth with apparently no catastrophic effects from inbreeding. (Then again, the end result is a whole new species of humanity, albeit a better species in many ways.)
Perelandra: It's another planet's version of Adam and Eve, but they still live in paradise and a world without sin or suffering.
A mild case occurs in Arrivals from the Dark when an alien race purchases a pair of eagles for their collection and releases them to roam on one of their preserve worlds (they live in orbital habitats). A century later, the eagles number in the hundreds and have adapted to the new world. This happens again, when another pair of eagles are taken from this world to a remote human colony on a world with a much harsher, colder climate. Despite this, the eagles once again increase their numbers and thrive.
Andrey Livadny's novel Ark is set aboard a Moon-sized (literally; it's actually the hollowed-out Moon with engines attached) Generation Ship sent a long time ago from Earth to find and collect alien life and put them in specially adapted habitats. A catastrophe kills the command crew and forces the rest of the humans to live in one of the habitats, leaving the ship's AI to fly the damaged craft. Over time, the humans regress to near-Medieval state and forget their origins. At the end of the novel, the Ark crash-lands into the sea on a habitable world orbiting a yellow dwarf, and the first person out is an old shepherd named Noah. How the ship ended up in the past is not explained. It is also not clear what happened to the aliens on-board.
The post-apocalyptic story "Mecanoscrit" by Manuel de Pedrolo ends with the creepy variant that the Adam-character dies, and the Eve-character wondering if she would live long enough to have her infant son grow up and have children with him, and a footnote stating that the entire story is a historical document. However, keep in mind that the entire story is written from Alba's ("Eve") perspective, save for the last episode, which is stated to be an analysis from a future investigator, who wonders about its authenticity but pretty much states that if what's on the text is true, then Alba is the mother of modern mankind.
With all the religious symbolism that shows up in Permutation City, it's only fitting that it should end with Paul and Maria setting off together into their own newly created universe.
In His Dark Materials, Lyra and Will end up being this at the end to ensure that Dust continues to flow down and into the worlds. Phillip Pullman even goes further with it and creates a serpent out of Mary Malone and a garden of Eden type world. In this case, what was important was not the mating and reproduction (they didn't produce a child together from their one time), but the act of intimately connecting to another sentient being and sharing/expressing the love they felt.
In Bob Shaw's short story "Call Me Dumbo", a family live in an isolated cottage, but it turns out that the parents were the sole survivors of a spaceship crash, and the mother was originally a man on whom the father performed a non-consensual sex change operation and suppressed his/her memory using drugs.
The ending of Invitation to the Game has the characters conclude that the eponymous Game's purpose is to train them as colonists for a new planet. However, they're True Companions with no romantic interest in each other... then they find another group, and realize several such groups have been placed on the new planet, close enough to form relatively accessible settlements, so there will be plenty of breeding material.
In After Doomsday, the women are well aware of the flaws of this reasoning; though they know that many people have survived, they are also aware that the men outnumber the women and make plans for polyandry so that every surviving woman will have children by several men.
Parodied in Eve Times Four when an officer on a spaceship makes this an Invoked Trope by 'accidentally' marooning himself on a planet with several attractive women (though one is somewhat older than he expected). They eventually figure out what he's up to, fix the Life Pod's engine and take off without him.
The short story "Procreation" by Gene Wolfe has a variant, and indeed a Shaggy God Story: the writer creates a miniature Universe. Deciding to let the creatures within know how they came to be, he and his sister ('Sis') write an account of the creation and drop it into the Universe. They don't know what to call the book, so just write their names on the cover: 'Gene' + 'Sis'.
"Born of the Sun" is a 1934 short story that is probably the reason why most editors had a policy of rejecting stories with this twist on sight. It starts out fine enough, with the heroes managing to build a spaceship to escape the Earth before it is destroyed, and they originally plan to defy this trope by saving as many people as they can. Unfortunately, it seems like the writer thought that he had no choice but to use the trope for this kind of story, because in the last few pages, the villain manages to whip up everybody except the male and female leads into a religious fervor and destroy the original spaceship, even though most of these people were volunteers who showed no sign of believing in the villain's cult at any earlier point in the story. Fortunately, the male and female lead have a smaller spaceship which they use to leave the Earth, but they are all alone. The implication is that their descendants will populate the universe, but then it runs into Fridge Logic that they wouldn't have enough genetic diversity to keep the species going, which the author seems at least vaguely aware of because of the aforementioned spoiler.
In the end of Sea of the Patchwork Cats, with Jen digested and Kara killed by the Queen of Cats, Conrad and Jaji are now the last human on the planet (if Jaji even counts), the ending having Jaji pregnant while Conrad contemplates the future.
In the ending of The Maze Runner trilogy, out of the entire human race, only a select few are able to resist the influence of the Flare virus. They are thus humanity's last hope to rebuild the Earth. However, that last few actually number several hundreds, which is far more, realistic than the usual application of this trope.
Richard Wilson's 1969 novelette "Mother to the World" is non-twist variation on the plot. A man and woman wake up one morning to find that everyone else in the world is gone. To complicate matters the woman is mentally disabled. The story revolves around their relationship and won the 1969 Nebula Award for Best Novelette.
In The Ice People, the civilization of Gondawa predicted its destruction and selected Éléa and Coban to repopulate Earth after the apocalypse. Coban was selected for his intellectual competence, while Éléa was selected for her attractiveness.
Averted with a vengeance in "The Last Man Alive" by Sutherland Neill of Summerhill school fame (and only added for notability, and being enforced by two-and-a-half): the half would be the Foregone Conclusion of the title, although one could weasel out on Exact Words ("man") here. Even more, the End Boss criminals shoot the girls (as avatars of the school children they are underage anyway) without a second thought for repopulation. But remember the book came out 1938, so even hinting at it, even if the criminals would have "waited" and jailed them somewhere for later abuse, would have been too sick for merely alluding to the possibility. So ultimately, the author avatar of Neill is the only one surviving. The school children, who co-worked on the book, of course call him out on the last fact, on which he dryly answers that he deserved it.
Subverted in The Genocides. A man and a woman do survive the novel, but are starving to death because the inedible Alien Kudzu has overrun the world.
Subverted in Gore Vidal's Kalki. The founder of a New Age religion gifts flowers to all the countries of the world as a sign of peace. They actually contain a deadly virus which kills everybody except Kalki and his chosen mate, Lakshmi, with whom he plans to start a new human race, and some elderly female followers and one elderly male biologist, who came up with the virus. They are all supposedly infertile. When Lakshmi turns out to be incapable of having children with Kalki, the biologist reveals he has been concealing Lakshmi and Kalki's incompatibility, and his own actual fertility, to become the father of the new world. Kalki kills the doctor, thus dooming the human race.
Discussed in The Last Day of Creation by Wolfgang Jeschke, which involves a time-traveling expedition stranded five million years in the past. While some are willing to breed with the Neanderthals, it's estimated that their genes will simply disappear in the millennia since. One group tries establishing a civilisation of Advanced Ancient Humans, but while they have the numbers needed to establish a viable colony, an estimated 20 to 30 thousand people would be needed to establish a civilisation, and most of those stranded have the wrong skills.
Frankenstein: Unbuilt Trope. Adam asks Victor to create a bride for him, but Victor refuses, arguing that there is no guarantee that they will be romantically or sexually compatible just because she is the same kind of undead abomination of science he is. Privately, Victor is more afraid of the opposite, namely that they will be too romantically and sexually compatible, and start populating the world with hyper-intelligent, superhumanly strong, people-hating monsters.
In "No Land of Nod", a 1952 short story by Sherwood Springer, a man and a woman are apparently the only survivors of a war involving nerve gas because they were in a sealed chamber for a space travel experiment. She's way ahead of the man on the implications and they have three daughters together. Before she dies, but she makes sure they never address the man as "father".
In The Purple Cloud, Adam and Leda are the only survivors of the titular Fog of Doom. For a while they form a Cynic–Idealist Duo, as Leda wants to restart the species but Adam thinks humanity deserves to die off. Leda wins in the end.
