BACKGROUND: Fars province lies to the south of the main foci of zoonotic cutaneous leishmaniasis (ZCL) caused by Leishmania major in central and northern Iran, and its ZCL foci might have emerged more recently because of different transmission cycles. However, there have been limited studies of the parasites infecting the regional sandfly vectors. METHODS: The diversities of sandflies and the Leishmania parasites infecting female sandflies were assessed for different habitats in Fars ZCL foci, 2008-2009, using standardized sandfly trapping and characterization of ribosomal DNA haplotypes of parasites. RESULTS: Vector diversity was similar to that in the main Iran ZCL foci, but parasite diversity was lower. Only Le. major was detected in Fars sandflies. Most infections were found in the abundant vector Phlebotomus papatasi collected in rodent burrows. Infections were detected for the first time in Iran in the related P. bergeroti. CONCLUSIONS: The failure to detect other gerbil parasites (Le. turanica, Le. gerbilli) is explained by the absence of one reservoir host, the great gerbil Rhombomys opimus. Other gerbils (Meriones species) may be the regional reservoir hosts, but transmission modelling is required for a better understanding of the emergence and stability of ZCL foci in Fars and other Iranian provinces.