In 2005, an epidemic of the cestode Triaenophorus crassus in Arctic charr, Salvelinus umbla from Lake Grundlsee (Austria) was reported, resulting in the closure of the local fisheries. The parasite uses a copepod and a salmonid fish as intermediate hosts, and the European pike (Esox lucius) as definitive host. In Lake Grundlsee procercoids of T. crassus, T. nodulosus and Eubothrium salvelini use the copepod Cyclops abyssorum praealpinus as their first intermediate host. We report on the development of a PCR-RFLP assay for the specific differentiation between the procercoids of the three cestode species. Ban I restriction sites within a 207-bp 18S rRNA-amplified fragment yielded two and three species-specific products to unequivocally distinguish between T. crassus and T. nodulosus, respectively. The assay is sufficiently sensitive to characterise a single procercoid of both Triaenophorus species in their copepod host, enabling a direct measure of infection. This assay will be useful in monitoring the progress of the control methods currently in place.