The validity of Gyrodactylus thymalli has been questioned, based on its morphological and genetic resemblance to G. salaris. This taxonomic problem has practical implications regarding correct diagnosis of G. salaris, which has proved to be highly pathogenic to stocks of wild Norwegian Atlantic salmon. The host specificity and pathogenicity of G. salaris and G. thymalli were experimentally tested on salmon and grayling. Both parasite species were able to infect, live and reproduce on both fish species. G. salaris was highly pathogenic for the experimental stock of salmon, while grayling mounted an effective response against this parasite. Both fish species responded to an infection with G. thymalli. The results did not support the hypothesis of conspecificity between G. thymalli and G. salaris. The ribosomal RNA gene intergenic spacer of both species was sequenced. Variation in sequence was lower than expected for different species. Variation in the sequences of tandemly repeated elements was found and may prove useful in distinguishing G. salaris and G. thymalli.