Molecular cloning techniques were used to identify genes encoding the proteolipids of putative vacuolar proton-transporting ATPases (V-ATPases; EC 3.6.1.35) of Entamoeba histolytica (Ehvma3) and Entamoeba dispar. The Ehvma3 gene encoded a 177-amino-acid peptide, with an M(r) of 18,110, which showed extensive positional identities with peptides of E. dispar (92%), Schizosaccharomyces pombe (58%), and humans (56%).