Few outbreaks of the desert sub-type of zoonotic visceral leishmaniasis (VL) have been described worldwide. In 2008, the incidence rate of VL in Jiashi County, Xinjiang Uygur Autonomous Region in the western part of the People's Republic of China, increased more than twenty-folds compared to the average annual incidence rate. The majority of the cases (96.6%) occurred among <2 year-old infants. For the first time in the desert area of Xinjiang, the parasites were isolated from bone marrow aspirates, using the NNN medium culture approach. The genetic analysis of the ITS-1 nucleotide sequence indicated that three isolates from eastern Jiashi County were genetically closely related and belonged to the Leishmaniainfantum group. However, they differed from an isolate from Kashi city which was classified as a member of the Leishmaniadonovani group.