Nucleotide sequences of nuclear ribosomal DNA internal transcribed spacers (ITS) were used to confirm morphological identification of Gyrodactylus species in Fennoscandia. Three pairs of morphologically similar or cryptic species are compared in this study. G. branchicus Malmberg, 1964 and G. rarus Wegener, 1910, hosted by the sticklebacks Gasterosteusaculeatus L. and Pungitiuspungitius (L.), respectively, displayed a genetic divergence of 0.9–1.3% along 774 nucleotides of ITS (Jukes & Cantor distance). G. branchicus isolates from the Baltic, White Sea and Scottish North Sea were invariable, but a Belgian North Sea population with a 0.4% divergence in ITS sequence has been collected. The species status of G. branchicus and G. rarus is supported by host-specificity in sympatric habitats and consistent morphological difference in the marginal hook sickles. Among Gyrodactylus on burbot Lotalota (L.) specimens were collected with their 792 bp long ITS sequences differing by 8.5%. This has led to the splitting of G. lotae Gusev, 1953 into two species, G. lotae and G. alexgusevi n. sp. The species are morphologically separable, and a similar range of variation was found in both the anchors and the marginal hooks in other collections and in the original description. Among G.macronychus-like parasites of minnow Phoxinus phoxinus (L.), divergent ITS sequences indicate two cryptic species. By comparison with the type-specimens, one was identified as G. macronychus Malmberg, 1957; the other is here designated as G. jussii n. sp., differing by 21.8% in 950–973 bp long ITS. The consequences of these findings for the species concept and species identification of Gyrodactylus are discussed.