The bloodsucking fly, Stomoxys calcitrans (Diptera: Muscidae), is a cosmopolitan pest that

transmits potential pathogens mechanically. We conduct phylogeographic analyses of

S. calcitrans to resolve its global population genetic structure for establishing baseline of

molecular studies. Results from mitochondrial gene suggested that the major divergence

of S. calcitrans predominantly occurred 0.32–0.47 million years ago (Mya) and the subsequent

diversifications took place during 0.13–0.27 Mya. The Ethiopian region was

deduced as the most likely origin of S. calcitrans and the Nearctic lineages were considered

to have originated from Oriental or Palaearctic regions. Our results further revealed

that each biogeographic region of S. calcitrans likely maintains its genetic specialty, and

yet, those non-monophyletic relationships were possibly caused by ancestral retention,

dispersal with mammals, long-distance migration, and the international livestock industries.

Moreover, the three highly diverged Ethiopian lineages may be putative cryptic

species that require clarification of their veterinary importance. Unravelling the genetic

structure of stable fly and preventing gene flow among biogeographic regions through

anthropogenic activities are thus pivotal in livestock industry administration, particularly

genetic exchange among differentiated lineages that might lead to the consequence of

ecological trait alterations.