Water buffalo species belongs to genus Bubalus and involves the wild and the domestic types. Domestic water buffaloes are reclassified into river and swamp types. Here, we have reconstructed the phylogenetic relationship between members of water buffalo species based on mitogenome sequences. The phylogenetic tree included lowland anoa, mountain anoain addition to wild, river and swamp water buffalo types.Results indicated the paraphyly of water buffalo species since lowland anoa and mountain anoa were clustered with river and wild water buffalo in a separate clade, leaving swamp buffalo at the outside. Results also indicated close genetic architecture between the mitogenomes of river and wild water buffalo types. These findings may indicate that river buffalo and swamp buffalo belong to two distinct species and that river buffalo and notswamp buffalo is a descendant of wild water buffalo.Mitogenome analysis provided more information about the taxonomic status of water buffalo types and verified their relationship with the members of genus Bubalus.