A new species of Haplosporidium Caullery & Mesnil, 1899 parasitising the pulmonate gastropod Siphonaria lessonii Blainville in Patagonia, Argentina, is described based on morphological (scanning and transmission electron microscopy) and sequence (small subunit ribosomal RNA gene) data. Different stages of sporulation were observed as infections disseminated in the digestive gland. Haplosporidium patagon n. sp. is characterised by oval or slightly subquadrate spores with an operculum that is ornamented with numerous short digitiform projections of regular height, perpendicular to and covering its outer surface. The operculum diameter is slightly larger than the apical diameter of the spore. Neither the immature nor mature spores showed any kind of projections of the exosporoplasm or of the spore wall. Regarding phylogenetic affinities, the new species was recovered as sister to an undescribed species of Haplosporidium Caullery & Mesnil, 1899 from the polychaete family Syllidae Grube from Japanese waters. The morphological characters (ornamentation of the operculum, spore wall structure, shape and size of spores, and the lack of spore wall projections) corroborate it as an as yet undescribed species of Haplosporidium and the first for the phylum in marine gastropods of South America. Siphonaria lessonii is the only known host to date.