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Pigs, the principal sources of meat for humans, have been crucial to cultures throughout Asia, especially in China and SE Asia, since prehistoric times. Several archaeological studies have used pig remains to elucidate the origin, culture, social evolution, and migration patterns of Asiatic people. However, ancient DNA of these remains in central SE Asia, and in Thailand in particular, has not been investigated to test the historical theories resulting from these archaeological studies. Here, we investigate ancient DNA of pig remains excavated from Pong Takhop archaeological site, central Thailand aged at least 3000 BP. The phylogenetic tree we obtained suggests that ancient Thai pigs were descended from ancient Chinese pigs. The tree topology further suggests that these ancient pigs had multiple origins, which were probably generated by multiple waves of migration of ancient Chinese pigs from 4000-3000 BP. Most of these ancient Thai pigs left their lineages as modern Thai pigs observed in northern Thailand. The contrasting cluster of pure modern Thai pigs suggested that these pigs might be descended from non-Chinese ancestors, possibly the native SE Asian ancestors.