Sixty-four Leishmania samples were isolated from patients in several villages in the Tataouine governorate, southeast Tunisia. This region is known to be a mixed focus of human cutaneous leishmaniasis caused by Leishmania (L.) killicki (synonymous L. tropica) and L. Major. To identify the Leishmania species in this governorate, a nested polymerase chain reaction based on the variable region of the kinetoplast minicircle was performed on each isolate. Multi-locus microsatellite typing using markers selected for their ability to amplify the two species was used to explore patterns of interspecific genetic exchange. Thirteen L. major and 51 L. killicki isolates were identified. The analysis of microsatellite data showed very low genetic diversity in each species with this set of microsatellites but a high differentiation between the two species. Nine L. major and five L. killicki strains revealed heterozygous genotypes with no shared allele between the two species. These heterozygotes probably resulted from genetic mutation events and not from interspecific genetic exchange. Specific and different epidemiological cycles at the sympatric level might explain the absence of genetic exchange between the two Leishmania species in the Tataouine governorate.