Phlebotomine sand flies are hematophagous insects that harbor bacterial, viral and parasitic agents like Bartonella sp., Phleboviruses and Leishmania spp., respectively. There are few reports on bacterial microbiota of Phlebotomus (P.) papatasi but no data available for natural populations of Turkey, where leishmaniasis is endemic. Therefore, we aimed to investigate the midgut bacterial flora of different populations of P. papatasi. Sand flies were collected from different towns (Karaburun, Urla, Ayvacik and Bascayir) located in the western part of Turkey. Laboratory reared P. papatasi were included in the study as an insectarium population. After sterile washing steps, sand flies were dissected and guts were separated. Three pools, (males, unfed females and blood-fed females) were generated for each population. Prokaryotic 16 S rRNA gene was amplified and DGGE was performed. Fourteen different organisms belonging to two Phylum (Proteobactericea and Furmicutes) were identified according to sequence results in the studied pools. The presence of Wolbachia sp. was shown for the first time in the wild-caught sand fly populations of Turkey. This is the first report of gut bacterial flora of wild-caught P. papatasi collected in an endemic area for leishmaniasis in Turkey. Microbiome profiling of wild-caught sand flies will be of great help in the investigating of possible vector control candidates for paratransgenic control approach.