Multiple realities(covers information from several alternate timelines)
An endangered species was a species which was on the brink of extinction, whether caused naturally or by the actions of sentient beings.
In an alternate timeline the Xindi succeeded in destroying Earth in 2154, rendering Humans an endangered species of roughly six thousand. (ENT: "Twilight")
Josiah, a member of the xenophobic organization Terra Prime, claimed in 2155 that Humans were becoming an endangered species due to the increasing presence of aliens on Earth. (ENT: "Demons")
In 2258 of an alternate reality, Spock considered himself part of an endangered species when Vulcan was destroyed by Nero, leaving an estimated (by Spock) 10,000 Vulcans still alive. (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")