Microsporidian infections are common in many fish species, yet detailed studies of these parasites in ecologically important wild populations are rare. Phylogenetic analysis using rDNA sequence data and parasite morphology indicate that mottled sculpin Cottus bairdii and slimy sculpin C. cognatus are hosts for Glugea sp. microsporidia in the northern USA. Glugea sp. is common in the Michigan populations sampled for this study, and prevalence was ≥70% in 4 of 6 infected populations (range ~4 to 80%). Glugea sp. infection causes the formation of xenomas associated with the body wall, fat body, gonads, and kidneys. Infections range from mild to very heavy, with variable xenoma numbers and sizes. Female sculpin experience heavier infections and more frequent infection of the gonads relative to males. Glugea sp. is transmitted horizontally between hosts through ingestion of spores. Vertical transmission may also be possible, either by spores infecting eggs directly or by spores contaminating the surface of eggs in the ovary or in the nest. The frequency and route of vertical transmission requires further study, but if it occurs, it may partly explain the high prevalence of infection. Our study combined with previous research suggests that additional molecular data and cross-infection experiments should be conducted to clarify species designations in the genus Glugea.