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• Gammarus lacustris is frequently infected with Microsporidia. • Dictyocoela was nearly exclusively found in G. lacustris from different locations. • RNA sequencing data can be used to search for microsporidian parasites. Microsporidia are a highly diverse group of single-celled eukaryotic parasites related to fungi and infecting hosts belonging to all groups of eukaryotes, including some protists, invertebrate and vertebrate animals. We investigated the diversity of microsporidia in the Holarctic amphipod species Gammarus lacustris from mostly, but not limited to, water bodies in the Lake Baikal region. Ribosomal DNA sequencing and host transcriptome sequencing data from various works show that this species is predominantly infected by representatives of the genus Dictyocoela and probably has some features underlying this specific interaction. [ABSTRACT FROM AUTHOR]