In 2003, the parasite fauna of 197 European eels Anguilla anguilla, captured at three different locations (Laufenburg, Karlsruhe and Beneeden Leeuwen) in the River Rhine, was analysed. The eels harboured a total of 18 species, among them the protozoa (Myxidium giardi, Myxobolus kotlani and Trypanosoma granulosum), acanthocephalans (Acanthocephalus anguillae, Acanthocephalus lucii, Echinorhynchus truttae, Pomphorhynchus laevis), nematodes (Paraquimperia tenerrima, Pseudocapillaria tomentosa, Camallanus lacustris, Raphidascaris acus, Spinitectus inermis and Anguillicola crassus), cestodes (Bothriocephalus claviceps and Proteocephalus macrocephalus) and monogeneans (Pseudodactylogyrus sp.). The parasite fauna at the different locations is discussed with respect to the crustacean fauna present at these locations. The investigation shows that changes in the composition of the crustacean fauna, due to the anthropogenic breakdown of a biogeographic barrier, are reflected in the composition of the intestinal eel parasite fauna.