We describe a novel sanguicolous parasitic ciliate, Metacollinia emscheri n. sp., found in the freshwater amphipods Gammarus pulex and G. fossarum. This ciliate infected 8.05 % of the amphipods collected in a German stream catchment, the Boye, a tributary of the river Emscher. The ciliate showed morphological characteristics fitting the genus Metacollinia. Different life stages of variable size occurred simultaneously in the hemocoel throughout the hosts’ body. The tomont had 40–47 slightly spiraled kineties, a non-ciliated cortical band, a large macronucleus, and contractile vacuoles arranged in rows or scattered throughout the cytoplasm. The protomites/tomites with nine somatic kineties presented evidence of the buccal kineties x, y, and z reminiscent of those of the order Foettingeriida. Phylogenetic analyses of the 18S rRNA and COI regions confirm the ciliate placement in the Collinidae and a close relatedness to the type species of the genus Metacollinia, Metacollinia luciensis.We formally describe this new parasite as Metacollinia emscheri n. sp. using pathological, morphological, and nuclear/mitochondrial genetic data. The systemic infections observed in histological preparations and the pathogenicity of Metacollinia emscheri n. sp. suggest that this parasite might influence host population dynamics. Given the ecological importance of amphipods as keystone species in freshwater ecosystems, an outbreak of this parasite might indirectly impact ecosystem functioning.