Although the strain causing cutaneous leishmaniasis (CL) in Sri Lanka was first identified in 2003, the strain causing visceral leishmaniasis (VL) has not yet been identified. We report the first isoenzyme typing of a strain causing VL in Sri Lanka at an early stage of emergence of VL in the country. The parasite was isolated from a 57-year-old civil soldier who had been in the jungle in the Vavuniya district in the Northern Province of Sri Lanka for a period of nearly 6 months immediately before the onset of symptoms. Multilocus enzyme electrophoresis (MLEE) revealed that the strain is Leishmania donovani zymodeme MON-37, the zymodeme which was previously identified from the CL patients in the country. The MLEE analysis was confirmed by sequencing the gene encoding the 6-phosphogluconate dehydrogenase isoenzyme. This is an instance of the same Leishmania zymodeme associated with both dermotropism and viscerotropism in the same geographic region. Further investigations into the genetic structure and identification of virulence factors in the parasite and immune factors in the host are required to understand the factors responsible for different tropism shown by the same zymodeme MON-37 L. donovani from Sri Lanka.