A single strain of Wolbachia (α-proteobacteria, Rickettsiales) was found in widespread geographical populations of each of two Phlebotomus species, within which there was no indication of ‘infectious speciation’. The two strains were identified by sequencing a fragment of wsp (a major surface protein gene), amplified by polymerase chain reaction from DNA extracted from the body parts of individual sandflies. Infection rates were high in the males and females of both sandflies, but they were lower for the B-group wPrn strain of Wolbachia in Phlebotomus perniciosus Newstead (60.3% overall) than for the A-group wPap strain in P. papatasi (Scopoli) (81.7%). Infections were frequent in the thorax, where Leishmania develops infective forms, as well as in the abdomen, where Wolbachia must infect the reproductive tissues to ensure its vertical transmission. These findings were related to knowledge of the population biology of Wolbachia in other insects, leading to the conclusion that this endosymbiont could be useful for driving transgenes through wild populations of both sandflies. This will require characterizing the cytoplasmic incompatibility phenotypes of Wolbachia–sandfly combinations, as well as estimating for them the incidence of paternal transmission and the fidelity of maternal transmission. Paternal transmission is one explanation for finding a single Wolbachia strain associated with all mitochondrial haplotypes and lineages of each sandfly species. However, this distribution pattern could also result from multiple horizontal transmissions or the failure of wsp to provide strain markers.