Trying to count them, so far.
1. The Great Allagan Civilization. Seems mostly based in Mor Dhorma but has outposts elsewhere.
2. The ones behind the Floating City of Nym in upper and outer La Noscea. Probably also behind the ruins in Camp Bronze Lake and the Wandering Palace.
3. The Amdapuri Civilization (Gelmorrans?). Located in the South Shroud and responsible for all the ruins there including Totorak and Amdapur Keep.
4. The civilzation in Southern Thanalan. Responsible for the Sepulchre, the Sunken Temple of Qarn and the Labyrinth.
Not sure if there is anymore.
Its not clear if these civilizations coexisted or existed and lived in different Astral Eras, but they probably died during the Umbral Eras.