In Dawnguard, Knight-Paladin Gelebor said that the Falmer had great temples to Trinimac, Syrabane, Jephre and Phynaster as well as to Auri-El (Although Auri-El's chantry is the greatest of them all).

The Falmer waged war against King Harald at least since 1E 140, and at the very most eighty years later were defeated at the Battle of the Moesring, forcing the Falmer to go into hiding. Syrabane, however, was known for saving Tamriel from the Thrassian Plague, which happened during 1E 2200. Even accounting for the then in-progress Dragon Break distorting time, that would still be around a millennium after the time when the Falmer ruled Skyrim, because I doubt the Dragon Break could alter any time before 1E 1200.