Dikerogammarus villosus is an invasive amphipod that recently colonized the main rivers of Central and Western Europe. Two frequent microsporidian parasites were previously detected in this species, but their taxonomic status was unclear. Here we present ultrastructural and molecular data indicating that these two parasites are in fact a single microsporidian species. This parasite shares numerous characteristics of Nosema spp. It forms elongate spores (cucumiform), developing in direct contact with host cell cytoplasm; all developmental stages are diplokaryotic and the life cycle is monomorphic with disporoblastic sporogony. Initially this parasite was described as Nosema dikerogammariOvcharenko and Kurandina 1987. However, phylogenetic analysis based on the complete sequence of SSU rDNA places the parasite outside the genus Nosema and it is therefore ascribed to a new genus Cucumispora. The key features characteristic to this genus are: presence of a very well-developed, umbrella-shape anchoring disk covering the anterior part of polaroplast; arrangement of isofilar polar filament into 6–8 coils convoluted with different angles, voluminous diplokaryon, thin spore wall and relatively small posterior vacuole containing posterosome. The parasite infects most host tissues but mainly muscles. It showed high rates of horizontal trophic transmission and lower rates of vertical transmission.