Abstract The introduction of freshwater fish species is a leading cause of aquatic biodiversity erosion and can spread parasites to native populations. Hidden diversity evidenced by recent taxonomic revisions can add further complexity to the issue by rendering biological assessment data incomplete. The Eurasian minnows Phoxinus are one such example of cryptic diversity, with several described species being invasive. Current non-native fish populations in the small Mediterranean island of Corsica (France) are the result of successive waves of introductions, including several Phoxinus species. This study aims at determining which Phoxinus species were introduced to Corsica using the cytochrome oxidase subunit I barcoding marker, reconstructing their introduction routes and examining their parasite communities. The study found four species in Corsica: Phoxinus phoxinus and Phoxinus csikii mainly in the northernmost studied drainage basin and Phoxinus dragarum and Phoxinus septimaniae in the Tavignano drainage basin. P. phoxinus and P. csikii were most likely introduced through a live bait wholesaler while P. dragarum and P. septimaniae were probably introduced by recreational anglers bringing their bait from continental France. The molecular study of their Gyrodactylus (Platyhelminthes: Monogenea) parasites with the ITS marker allowed us to hypothesize inter-drainage basin secondary introduction routes for P. phoxinus and P. dragarum . In several sampling sites, Phoxinus minnows had black spot disease caused by encysted metacercariae of Digenea, likely Posthodiplostomum cuticola . These parasites were also found on the brown trout Salmo trutta in a locality where this patrimonial species co-occurs with Phoxinus minnows. Barcoding should be used in fish communities monitoring to help to accurately identify cryptic species.