Water buffalo is an important livestock species in Asia as well as in the world. The swamp type buffalo, found throughout southeast Asia, from Assam and Nepal in the west to the Yangtse valley of China, is traditionally reared to produce draft power and meat. In this study, microsatellite markers were analyzed to determine genetic origin and population relationships of swamp buffalo in China and south-east Asia. Results showed that populations in south-east Asia and southwest of China had highest level of genetic variability. Differentiation among the Chinese swamp populations was much less than among the southeast Asian. Relationships among the swamp populations (DA genetic distances and STRUCTURE analyses) show the southeast Asian populations separated into two groups by the Chinese populations. Given these relationships and the patterns of genetic variability, we postulate that the swamp buffalo was domesticated in the region of the far south of China, northern Thailand and Indochina. Following domestication, it spread south through peninsular Malaysia to Sumatra, Java and Sulawesi, and north through China, and then to Taiwan, the Philippines and Borneo.