Babesia leo, a small piroplasm isolated from lions in South Africa is described as a distinct species based on a phylogenetic analysis of the 18S rRNA gene. Intraerythrocytic trophozoite and merozoite stages of B. leo are morphologically indistinguishable from other small piroplasms of felids. Previous studies showed that B. leo was biologically and antigenically distinct from B. felis, which is known to infect wild and domestic felids in South Africa. Molecular characterization showed strong support for the phylogenetic seperation of B. leo as a distinct species from B. felis and other felid piroplasms. Phylogenetic analysis also showed that Babesia microti and all of the felid piroplasms from Africa with known 18S rRNA gene sequences available, including B. leo, formed a single, separate clade, sister to the other babesial and theilerial piroplasm parasites.