BACKGROUND: The ongoing kala-azar elimination program in Nepal is based on the assumption of anthroponotic transmission of the protozoan parasite Leishmania donovani. This parasite species was recently also found in lesions of cutaneous leishmaniasis (CL) cases, which are increasingly reported mainly from western Nepal. The question whether or not CL causing L. donovani can also contribute to VL is a crucial one to answer if the success of the VL elimination initiative in the Indian subcontinent is to be sustained, though evidence on sub-species level genomic differences between CL and VL causing L. donovani is currently lacking. This study aims to provide a genomic comparison of L. donovani parasites currently causing CL in Nepal with previously described L. donovani isolates. METHODS: A case series study was carried out in sentinel dermatological sites in Western Nepal. Skin punch biopsies were collected from clinically suspected CL lesions. Molecular tests based on the ribosomal RNA gene array were used to detect and characterize the Leishmania parasites. RESULTS: Leishmania parasites detected in 26 cutaneous leishmaniasis patients were identified as L. donovani. Importantly, their analyzed DNA sequences were identical, and shared with previously documented sequences from both cutaneous and visceral disease-causing parasites in Nepal, India and Bhutan. CONCLUSIONS: Our study suggests that CL and VL are caused by similar if not identical L. donovani parasite strains, though additional sequencing is required to corroborate this finding. If confirmed, cutaneous lesions could act as a kala-azar parasite reservoir, which would have important implications for the kala-azar elimination program.