OBJECTIVE: To identify and understand the natural transmission cycles of Leishmania in Iranian sandflies. METHOD: Nested PCR protocols were developed to amplify two regions of the ribosomal RNA amplicon of Leishmania (ITS1-5.8S rRNA gene, and a microsatellite DNA region of ITS2), which were species-specific by DNA sequence or fragment size. RESULTS: The PCR assays detected in Iranian sandflies not only Leishmania major but also for the first time L. turanica and L. gerbilli sensu lato, two other parasites of the great gerbil. All three parasites were found in the northeast and centre of Iran, in two foci of rural Zoonotic Cutaneous Leishmaniasis (ZCL) caused by L. major. Fifty infections were detected in common sandfly species: at least six geographically differentiated haplotypes of L. major in four to five sandfly species; one strain of L. gerbilli s.l. in five to six sandfly species and one strain of L. turanica in one sandfly species. CONCLUSION: Past conclusions about the transmission cycles of L. major in Iran should be treated with caution. Careful molecular eco-epidemiological investigations are essential for modelling the roles of different sandfly species in maintaining and spreading ZCL foci. Even if non-pathogenic to humans, frequent inoculations of L. turanica by sandflies might alter the efficacy of vaccines against L. major. Phlebotomus papatasi is probably the key vector in many ZCL foci because of its abundance and high infection rates with both L. major and L. turanica.