This paper undertakes a major survey of the genus Sus from Island Southeast Asia and specifically attempts to re-examine the taxonomic status of the pigs of Wallacea, in order to re-evaluate the complex evidence for human mediated dispersal. This was undertaken using the combined approach of tooth outline and mitochondrial DNA analysis. The data provide clear evidence for three dispersal events: The first involved domesticated pigs, originating from wild Sus scrofa stock in mainland Southeast Asia, being introduced to the Greater and Lesser Sunda Islands, to the Mollucas, New Guinea, and Oceania. Archaeological specimens clearly link these pigs with the Lapita and subsequent Polynesian dispersals. Since the pigs on New Guinea are specifically linked with this dispersal, it follows that the current wild populations of the island must be the feral descendants of introduced domestic pigs from mainland Southeast Asia, which came into New Guinea via the Lesser Sunda Islands. A second dispersal event also involved domesticated pigs (this time from wild Sus scrofa populations from mainland East Asia), introduced to the Philippines and Micronesia, while a third involved the endemic warty pig of Sulawesi (Sus celebensis), which data from Liang Bua cave shows was introduced to Flores perhaps as early as 7000 B.C.