Fine and dandy.
Now, let's take another case: you know species A, you know nothing about B and C. Thus you can tell "A was here" but... can you tell there are other (exactly) two that "were here" as well? Maybe they were only one, maybe more than two. How can you tell?
Welp, that's exactly the problem, that isn't to say there aren't other methods though. For example you could see how much genetic differentiation there is between known species in the area and make assumptions based on that. You could also use other types of DNA, mitochondrial DNA for example which may tell a different story.
Fact is, taxonomists are always fighting about which species is which, sometimes with fruition. DNA, while it is very useful in determining one species from another has added to the questions about what really defines a species and what differentiates one from the other. Even morphologically there has been debate as to whether the two specimens you are holding are one species or two. Take the Eclectus Parrot for an early example, the male is bright green whereas the female is red/purple, scientists thought them to be separate species until they actually saw them mating. Things can get even more confusing when species don't physically mate with each other (think pollen and plants) or when they mate between species. Hopefully this type of science will take us closer to the answer.
On the other hand, personally I like these kind of studies for other uses like saying "Hey! This spot has way more genetically different organisms, maybe it's more important to not pollute it"