The genus Bartonella encompasses several zoonotic species that cause emerging infectious diseases in humans. These species are transmitted to humans by hematophagous arthropods. In South America, sand flies are the most important vectors of Bartonella bacilliformis, the etiological agent of Verruga peruana. Due to the importance of bartonellosis in public health, the aim of this study was to detect Bartonella in wild populations of phlebotomine sand flies in southern Mexico. In total, 29 sand flies belonging to 6 species were collected. Only 2 specimens were positive, representing a prevalence of 8.69% (2/23). This appears to be the first report of Bartonella sp. in phlebotomine sand flies outside the endemic area of Verruga peruana in South America. Further studies are needed to clarify the relation between this bacterium and sand flies in Mexico.