Based on morphological, morphometric, and molecular data, we describe a new hemoparasite of the genus Haemogregarina Danilewsky 1885, isolated from the Brazilian aquatic turtle Podocnemis unifilis (Testudines: Podocnemididae). The new species, Haemogregarina podocnemis sp. nov. (Apicomplexa: Haemogregarinidae), is characterized by small trophozoites with a single cytoplasmic vacuole on one side; pre-meronts with nuclear chromatin dispersed in the cytoplasm, with or without cytoplasmic vacuoles; meronts that are usually broad and slightly curved (kidney-shaped), with an average of eight small rectangular nuclei; immature gamonts (bean-shaped) with two morphological types: one with nuclear chromatin dispersed in the cytoplasm and the other with nuclei in the middle of the cell; mature gamonts of two morphological types: one with a length equal to or greater than that of the erythrocyte and the width of the nuclei similar to that of the hemoparasite and the other smaller than the erythrocyte with the width of the nuclei less than that of the hemoparasite. This is the first hemogregarine species described that infects the Brazilian turtle Po. unifilis. These findings highlight the need for further studies of Haemogregarina spp. to better determine the biodiversity of this understudied parasite group.