The microhabitat selection of the ectoparasite Gyrodactylus salaris (Laerdalselva strain, Norway) was investigated concurrently with studies on the parasite population growth on five strains of Atlantic salmon, Salmo salar L., and a strain of Danish rainbow trout, Oncorhynchus mykiss (Walbaum). The salmon used were hatchery-reared parr of East Atlantic strains [River Conon (Scotland), River Storå (western Denmark) and River Atran (western Sweden)] and Baltic strains [Lule and Ume (eastern Sweden)]. The location and numbers of parasites were recorded on anaesthetized fish once a week from week 0 to week 8. The mean abundance of G. salaris steadily increased to high levels on the River Conon, Storå and Atran strains until the end of the experiment. The mean abundance of G. salaris on the two Baltic strains (River Lule älv and River Ume älv) initially increased but after 4-7 weeks the growth of the parasite infrapopulations decreased markedly. The Danish rainbow trout strain showed the lowest abundances of all the fish species and strains. Gyrodactylus salaris preferentially selected the fins and head region when colonising the hosts (all species and strains). Increasing percentages of G. salaris on the tail fins of the East Atlantic strains and rainbow trout were found during the course of infection, whereas the two Baltic salmon strains experienced a decreasing percentage of parasites in this microhabitat.