Multilocus enzyme electrophoresis (MLEE) is the gold standard for taxonomy and strain typing of Leishmania, but has some limitations. An alternative reliable and fast genotyping method for addressing population genetic and key epidemiological questions, is multilocus microsatellite typing (MLMT). MLMT using 15 markers was applied to 91 strains of L. donovani, L. archibaldi, L. infantum and L. chagasi from major endemic regions of visceral leishmaniasis. Population structures were inferred by combination of Bayesian model-based and distance-based approaches. Six main genetically distinct populations were identified: (1) L. infantum/L. chagasi MON-1 and (2) L. infantum/L. chagasi non-MON-1, both Mediterranean region/South America; (3) L. donovani (MON-18), L. archibaldi (MON-82), L. infantum (MON-30, 81) and (4) L. donovani (MON-31, 274), L. archibaldi (MON-82, 257, 258), L. infantum (MON-267), both Sudan/Ethiopia; (5) L. donovani MON-2, India; (6) L. donovani (MON-36, 37, 38), Kenya and India. Substructures according to place and time of strain isolation were detected. The VL populations seem to be predominantly clonal with a high level of inbreeding. Allelic diversity was highest in the Mediterranean region, intermediate in Africa and lowest in India. MLMT provides a powerful tool for global taxonomic, population genetic and epidemiological studies of the L.donovani complex.