The amphipod crustacean Gammarus duebeni hosts two feminizing microsporidian parasites, Nosema granulosis and Microsporidium sp. Samples of G. duebeni were collected from three sites on the Scottish island of Great Cumbrae and screened for microsporidia using polymerase chain reaction. Associations between the prevalence of the two feminizing parasites and haplotypes of the host mitochondrial gene cytochrome oxidase I (COI) were investigated. The prevalence of both parasites varied significantly among the host's COI haplotypes, suggesting that horizontal transmission is rare or absent in the life cycles of the feminizing microsporidia and that all transmission must therefore be vertical. Life cycles in which all transmission is vertical are common among bacterial parasites but have never before been demonstrated in Eukaryotic parasites.