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Background   Phlebotomus papatasi  sand flies are major vectors of  Leishmania major  and phlebovirus infection in North Africa and across the Middle East to the Indian subcontinent. Population genetics is a valuable tool in understanding the level of genetic variability present in vector populations, vector competence, and the development of novel control strategies. This study investigated the genetic differentiation between  P. papatasi  populations in Egypt and Jordan that inhabit distinct ecotopes and compared this structure to  P. papatasi  populations from a broader geographical range .Methods  A 461 base pair (bp) fragment from the mtDNA cytochrome  b  ( cyt b ) gene was PCR amplified and sequenced from 116 individual female sand flies from Aswan and North Sinai, Egypt, as well as Swaimeh and Malka, Jordan. Haplotypes were identified and used to generate a median-joining network,  F   ST   values and isolation-by-distance were also evaluated. Additional sand fly individuals from Afghanistan, Iran, Israel, Jordan, Libya, Tunisia and Turkey were included as well as previously published haplotypes to provide a geographically broad genetic variation analysis.    Results  Thirteen haplotypes displaying nine variant sites were identified from  P. papatasi  collected in Egypt and Jordan. No private haplotypes were identified from samples in North Sinai, Egypt, two were observed in Aswan, Egypt, four from Swaimeh, Jordan and two in Malka, Jordan. The Jordan populations clustered separately from the Egypt populations and produced more private haplotypes than those from Egypt. Pairwise  F   ST   values fall in the range 0.024–0.648.    Conclusion  The clustering patterns and pairwise  F   ST   values indicate a strong differentiation between Egyptian and Jordanian populations, although this population structure is not due to isolation-by-distance. Other factors, such as environmental influences and the genetic variability in the circulating  Le. major  parasites, could possibly contribute to this heterogeneity. The present study aligns with previous reports in that pockets of genetic differentiation exists between populations of this widely dispersed species but, overall, the species remains relatively homogeneous.    Electronic supplementary material  The online version of this article (10.1186/s13071-018-2785-9) contains supplementary material, which is available to authorized users.

Population genetics analysis of Phlebotomus papatasi sand flies from Egypt and Jordan based on mitochondrial cytochrome b haplotypes