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The Labyrinthulomycota are a relatively poorly studied group of heterotrophic unicellular eukaryotes. They comprise three lineages, labyrinthulids, thraustochytrids, and aplanochytrids, which are all primarily marine organisms and considered to be important components of marine microbial communities. Recently a number of Labyrinthulomycota have been implicated as parasites of marine (but also terrestrial) plants and marine molluscs. Here we describe a new species of thraustochytrid, Thraustochytrium caudivorum sp. nov. that we have isolated from laboratory cultures of Macrostomum lignano (Rhabditophora, Macrostomorpha), a marine free-living flatworm. In these worms T. caudivorum can cause lesions, which start at the tip of the tail plate and which can lead to the dissolution of the posterior part of the animal. Although the worms can frequently cure these lesions and regenerate the lost parts, the lesions can also result in the complete dissolution of the animal. We describe this thraustochytrid based on pure agar cultures and infestations in the worm cultures. Moreover, we describe its pathological effects on the worms and its morphology using both light and electron microscopy. In addition, we report a phylogenetic analysis using a partial 18S rDNA sequence that allows us to place this new species within the thraustochytrids. Finally, we outline a protocol that allows to permanently remove the parasites from infested worm cultures. We conclude that thraustochytrids represent a novel group of parasites of free-living flatworms.