The monogenean flatworm Gyrodactylus thymalli (Zitnan, Helminthologia, 2:266-269, 1960) is considered a harmless ectoparasite on grayling (Thymallus thymallus). The species is closely related to G. salaris Malmberg, 1957 that causes severe gyrodactylosis on Atlantic salmon (Salmo salar) in many Norwegian rivers. In this paper, we study the mitochondrial diversity of a G. thymalli population from one of the type localities Hrable on River Hnilec, Slovakia. By sequencing parts of the mitochondrial NADH dehydrogenase subunit 5 gene, we detected three haplotypes that differ from each other by 2.1-4.1%. The haplotype HnilecI was found most common. Our data suggest that River Hnilec has been colonized independently at least three times with G. thymalli.