A central prerequisite for control of food-borne zoonotic trematodes is an accurate diagnosis at least at genus level. Freshwater fish muscles can harbor metacercariae of species that differ in zoonotic importance and that cannot be distinguished with conventional light microscopy due to the small size of these metacercariae. These parasites cannot be visually detected in fish and monitoring requires expert application of time-consuming techniques. The multiplex PCR developed in ParaFishControl will provide a rapid and cost-effective tool for the simultaneous identification of O. felineus, P. truncatum, Metorchis spp., Metagonimus spp. and Apophallus spp. the main zoonotic or potentially zoonotic trematodes present in Europe. This multiplex PCR can be used to identify the abovementioned genus/species at any developmental stages. This multiplex PCR is an accurate and affordable method that avoids the costs of sequencing and enables rapid identification of any developmental stage of five potentially zoonotic in a single reaction. The diagnostic tool has been developed and validated and is now being offered as a service of the University of Bologna.