So, there are many species that are considered very rare, but are most likely extinct, because they haven't been seen for a while. I'm not going to consider those species.

I'm going to look at a species for which we only know of 2 living specimens.

Yangtze Giant Softshell Turtle (Rafetus swinhoei), family Triochychidae, once inhabited river systems and lakes in Eastern and Southern China

CRITICALLY ENDANGERED.

There are, most likely, only 2 individuals left in the world. (They are both males).

This is considered by some, to be the largest freshwater turtle in the world, weighing in at up to 100 kg (220 lbs). This is the largest verified spcimen, others may have been larger, reportedly.