What do you mean when a girl says that she's an endangered species?

Maybe she meant that she is unique and unlike anyone.

Depends on her age. It could be a reference to her virginity if she's a teenager

If she is like 16+ then the chances are that the rest of her friends are not virgins anymore, and she could be one of the only one of her friends that still is, thus the reference to endangered species.

Is this applicable?

If you didn't understand what she meant, why didn't you just ask her? there is nothing wrong with not knowing something. asking is how you learn. you already know she is not an endangered species, you can't be expected to guess why she said that.

She means that she will vanish anytime and will not born again and there will be nobody else like her available on this earth therefore whatever you wish to do with her do it fast and enjoy yourself.

I would start calling her chunky cause only fat ugly girls say that. But no I'm serious about my last question