In this population genetic study of Leishmania donovani parasites in the Indian subcontinent, 132 isolates obtained from patients in Bangladesh, India, Nepal and Sri Lanka suffering from Kala-azar (100), post-Kala-azar dermal leishmaniasis (PKDL) (25) and cutaneous leishmaniasis (CL) (2), and from 5 patients whose clinical patterns were not defined, were analysed by using 15 hyper-variable microsatellite loci. Multilocus microsatellite typing (MLMT) data were analysed by using a Bayesian model-based clustering algorithm and constructing phylogenic tree based on genetic distances. In total, 125 strains from Bangladesh, Bihar (India) and Nepal formed a very homogeneous population regardless of geographical origin, clinical manifestation, and whether they presented in vitro or in vivo susceptibility to antimonial drugs. Identical multilocus microsatellite profiles were found for 108 strains, other strains differed in only one marker. Considerably different microsatellite profiles were identified for three Indian strains most closely related to L. donovani from Kenya, and for four strains from Indian and Sri Lankan CL cases. The circulation of a single homogeneous population of L. donovani in Bihar (India), Bangladesh and Nepal is, most probably, related to the epidemic spread of visceral leishmaniasis in this area.