Multilocus molecular and phylogenetic analysis of phlebotomine sand flies (Diptera: Psychodidae) from southern Italy

► We conducted a molecular and phylogenetic analysis of sand flies from southern Italy. ► We analyzed mtDNA and rDNA gene sequences of five common sand fly species. ► We found eight mitochondrial haplotypes and three ITS2 sequence types. ► Mean level of interspecific divergence was 16% for mtDNA and 25% for ITS2. ► Multilocus sequencing is a tool for the molecular identification of sand flies.