Molecular analysis based on mitochondrial DNA (mtDNA) sequence was performed to elucidate the genetic di#erence between Haematobia irritans (Linnaeus) and H. exigua (de Meijere), and the phylogenetic relationship among Japanese Stomoxyini species (Stomoxys calcitrans (Linnaeus), S. indicus Picard, S. uruma Shinonaga et Kano, and Haematobosca sanguinolenta (Austen) including Haematobia). Two populations obtained from Obihiro and Morioka which were morphologically identified as H. irritans were genetically identical. Two populations obtained from Taiwan and Vietnam which were morphologically identified as H. exigua were almost genetically identical, but there was a small divergence (0.3῍0.4῎) between them. Nucleotide sequence divergences between H. irritans from Obihiro-Morioka and H. exigua from Taiwan-Vietnam were 1.8῍1.9῎, and those between Haematobia and other separate species of Stomoxys and Haematobosca were 6.7῍10.9῎. In cluster analysis based on mtDNA, Haematobia species were close to Haematobosca sanguinolenta. S. calcitrans and S. uruma were closely related to each other, and S. indicus was distantly related to these two species. We discussed the status of H. irritans and H. exigua based on mtDNA, and the discrepancies of molecular phylogeny versus the previous hypotheses based on morphological criteria in Japanese Stomoxyini.