Myxozoan parasites of the genus Kudoa Meglitsch, 1947 are associated with post-mortem tissue degradation that causes great financial losses to commercial fisheries. Kudoa thyrsites (Gilchrist, 1924) is a species with a very wide host range including commercial tunas, mackerels, salmonids and flatfishes. A sample of 190 fishes of 18 species from the Madeira Archipelago and 30 Atlantic chub mackerel, Scomber colias Gmelin, and 30 blue whiting, Micromesistius poutassou (Risso), from the Portuguese mainland coast were examined for the presence of species of Kudoa. The prevalence of Kudoa spp. was 80% in M. poutassou and 60% in S. colias. No spore was detected in S. colias from Madeira, which was confirmed by specific PCR screening of the muscle from all individuals of S. colias. SSU rDNA analysis revealed that M. poutassou and S. colias from the Portuguese mainland coast were infected with K. thyrsites, an economically important myxozoan parasite. Both sequences were identical with sequences of the eastern Atlantic K. thyrsites genotype, including that from the type host of this parasite. This is the first report of K. thyrsites from M. poutassou and S. colias. The fact that spores of species of Kudoa were not detected in fishes screened in the Madeira Archipelago may be explained by various ecological factors, such as the absence of a continental shelf, a short insular shelf, and oceanic waters with low productivity, all resulting in reduced abundance of benthic organisms. Consequently, it is possible that as yet unknown annelid definitive hosts of Kudoa spp. are absent or very rare near Madeiran coasts.