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The genetic structure of the most abundant species in the genus Eubothrium, E. crassum and E. salvelini, was studied by allozyme analysis in order to provide a consistent diagnosis for these morphologically similar species, as well as to assess their genetic relatedness. The proportion of fixed allelic differences (56.3%, 9 of 16 loci) between the species falls within the range accepted for valid species. A strict host specificity of E. crassum and E. salvelini for their typical host (lake trout, Arctic charr, respectively) was found in the French localities examined (Lake Annecy, Lake Bourget). For E. salvelini, polymorphism with the established allelic profile was found in the acid phosphatase (ACP) system. No significant deviation from the Hardy-Weinberg equilibrium expectations for ACP were found in either of the E. salvelini populations, which suggests predominantly cross-fertilization of these hermaphrodites. Analysis of the standardized variance in allelic frequencies demonstrated almost no among population differentiation (estimator θ of F st=−0.03) between E. salvelini populations.