Henneguya malabarica sp. nov. is described from the Amazonian teleost fish Hoplias malabaricus Boch, 1794, collected from the estuarine region of the Amazon river near Belém, Brazil. Plasmodia were represented by several vegetative nuclei, generative cells, and sporogony stages contained in cyst-like plasmodia. The spore body was ellipsoidal (12.6 microns in length and 4.8 x 3.6 microns in width) and each valve presented a tapering tail (17.1 microns in length). Thin valves surrounded the binucleate sporoplasm cell and two spherical polar capsules (3.7 x 1.8 microns) that contain five to six coils of the polar filament. The spore had an iodinophilous vacuole. The basal portion of the spore body of immature and mature spores and the whole surface of the tails were surrounded by a close homogeneous sheath. The prevalence of infection was 6.7% in the fish examined. The spores differed from those of previously described species of Henneguya in their shape, size, spore, and arrangement of the polar-filament coil. The taxonomic affinities of this parasite to other species are discussed.