This is a list of fictional ancient extraterrestrial species in science fiction who have all but died out, left only ruins or have only a small group of survivors left:
Ahamkara (Destiny)
Ancient humanoids (Star Trek)
Alteran (Stargate)
Ancient / Lantean (Stargate)
Ori (Stargate)
Ancient (Descent: FreeSpace – The Great War)
Ancient (Farscape)
Ancient (Traveller)
Asgard (Stargate)
Assassin (The Heechee Saga)
Arisian (Lensman)
Celestial (Marvel Comics)
Celestial (Star Wars)
Chozo (Metroid)
Cocytan (The Dig)
Eddorian (Lensman)
Elder God (H. P. Lovecraft)
Faranji from Star Sonata
The First Ones (Babylon 5)
Forerunner (Halo)
Furling (Stargate SG-1)
Ganymeans (Giants series)
Hanshak (Ascendancy)
Heechee (The Heechee Saga)
Iconian (Star Trek)
Jjaro (Marathon)
Kimera (Earth: Final Conflict)
Leviathan (Mass Effect)
Metron from Star Trek:TOS
Mzungu from Star Sonata
Necrontyr (Warhammer 40,000)
Nox (Stargate SG-1)
Oan (DC Comics)
Nebula, the (Andromeda)
Occlith (Clark Ashton Smith)
Old Ones (Warhammer)
Old Ones (Warhammer 40,000)
Old Ones/Elder Things (H. P. Lovecraft)
The Overmind (Childhood's End)
Paradine (Andromeda)
Psionics (Notrium)
Precursor (Star Control)
Precursor (Halo)
The Progenitors of (Homeworld 2)
Prothean (Mass Effect)
Protoculture (Macross)
Rakata (Star Wars)
Reapers (Mass Effect)
Shadow (Babylon 5)
Shipwrights, the creators of Mother (Remnants)
Thrint or "Slavers", ancient rulers of the Galaxy (Known Space)
T'kon (Star Trek)
Thran (Magic: The Gathering)
UrQa from Star Sonata
Vazaha from Star Sonata
Vex (Destiny)
Voorqual (Clark Ashton Smith)
Vorlon (Babylon 5)
W'rkncacnter (assuming there is more than one) (Marathon)
Watcher (Marvel Comics)
Xel'Naga (StarCraft)
Xeelee (Xeelee Sequence)
Unnamed and unseen aliens in the Space Odyssey series (In the prologue of 3001: The Final Odyssey they are called the "Firstborn", but never referred to as such in-story in any novel in the series.)
Ancients (Ice Age: Collision Course) named by Buck; made the Scrat's UFO and the Prophetic tablets