Gyrodactylus thymalli Zitnan, 1960 and G. salaris Malmberg, 1957 have an indistinguishable ribosomal internal transcribed spacer (ITS) DNA sequence, but exhibit surprisingly high levels of intra- and interspecific sequence variation of the mitochondrial cytochrome oxidase I (CO1) gene. To test whether different populations of these reportedly very similar species could be discriminated using morphometric methods, we examined the morphometry of four different populations representing different mitochondrial clades. Twenty five point-to-point measurements, including five new characters of the attachment hooks, were recorded from three Norwegian laboratory populations (G. salaris from the Rivers Lierelva and Rauma, and G. thymalli from the River Rena), and from one wild population of G. thymalli from the River Test, UK. The Norwegian populations were kept under identical environmental conditions to control for the influence of temperature on the haptoral attachment hooks. Data were subsequently subjected to univariate and linear stepwise discriminant analyses. The model generated by the linear stepwise discriminant analysis used 18 of the 25 original variables, the first two roots accounting for 96.6% of the total variation between specimens. The hamulus shaft length accounts for 66.7% of the overall correct classification efficiency. Based on morphometry, all specimens were assigned to the correct species. Apart from three specimens of G. salaris from the River Lierelva population which were misclassified as belonging to the G. salaris Rauma population, all specimens were assigned to the correct population. Thus, populations of Gyrodactylus identified by mtDNA can also be discriminated using morphometric landmark distances.