The plural form of species is species. The plural possessive form of species is species'. So your sentence is correct. I think if you were referring to multiple species you could use other context clues to inform the reader that you are talking about more than one species such as:
"All of the species' ears are notably fuzzy."
If I were reading a paragraph about more than one species and I encountered this sentence I would make the assumption that you were referring to all of the species being spoken about rather than one individual species.
It might be easier to reword the sentence to something like this: "The two [or more] species have fuzzy ears.
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