An endangered species is a species which is on the brink of extinction, whether caused naturally or by the actions of sentient beings.
In 2258 of an alternate reality, Spock considered himself part of an endangered species when Vulcan was destroyed by Nero. (Star Trek)
Corvan gilvos were endangered by the pollution of their native habitat on Corvan II. In 2368, there were only fourteen remaining. (TNG: "New Ground")
In an alternate timeline the Xindi succeeding in destroying Earth, rendering Humans an endangered species of roughly six thousand. (ENT: "Twilight")