Mixed fish farming, where different fish species live together, promotes lateral transfer of parasites. However, to be sure that it is the same species, morphological study alone is not enough to conclude.
Wow! This is a very interesting question and valuable project that would ensure the preservation of aquatic biodiversity! Congratulations. Indeed, you are right, only morphological study will not be enough. Other molecular tools are required for such project! The attached paper will enlighten you of other suitable molecular tools for determining and characterizing the populations of parasitic crustacean species. Best regards