If they can extract good DNA it is relatively easy. DNA breaks down over time (relatively quickly relative to geological time) so the really old stuff won’t have usable DNA. If the bone shapes do not match the expected shape of an animal of a known species they may attribute the difference to being a new species. They have to try and rule out natural deformities and differences due to age. The more different the shape from the expected (after ruling out deformities or age related size issues) the more certain that it is from a different species.
There have been numerous cases where something originally classified as a different species was found to actually have been part of an existing species after later examination.
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