Over the course of its long run, many of the songs and soundtracks from The Mysterious Cities of Gold have become well known, and as iconic as any plot point.
- Perhaps the most iconic of the songs is, naturally, the theme song.
Both the original and the second season opening share an upbeat quality to them that call the viewer to come and join on an epic adventure. Even the third season opening gets in on the action, seeming to blend elements of the first two season's themes. - Saint Elmos's Fire is a strange and mystical song that perfectly illustrates the mystery of the things that the group encounter.
- Of particular note is the Song of Mysterious Awesomeness, which plays during the reveal of the Golden Condor, as well as earlier in the series with the golden butterflies.
- "Goodbye, Father", the sad variant of the opening theme (not to be confused with a track named "Sad Cities of Gold") that plays during any particularly heartbreaking or sad moment. It also plays in season two when Tao is speaking with Ambrosius about Esteban's Atlantean heritage.
- "Theme of Tao" is an upbeat island remix of the main theme. It plays in episode 18 of season 2 after Esteban is saved from the scorpion and the children are heading back to the Condor.
- Much of the synth music qualifies, giving the series a strange and mysterious feeling. While subdued in later seasons, it is still present and always a treat to hear.
