Abstract: AFLP markers were detected by the two-color fluorescent detection in a sample of DNA pool of 21 Asian native pig populations, 19 European and American commercial pig populations, 5 wild pig populations, 1 Duroc×Chinese wild pig hybrid population and 1 Chinese sythetic pig breed. 312 polymorphic markers were detected by a total of 22 AFLP primer combinations. The genetic similarity coefficients of 47 pig populations were calculated from AFLP data, and molecular phylogenetic tree was constructed by UPMGA method. The results showed that Chinese native and wild pig populations had remarkable genetic differentiation with European and American commercial pig populations and wild pig populations, indicating that Chinese native pig populations may originate from Asian wild pigs, while European and American commercial pig populations were domesticated from European and American wild pigs. Although different populations of commercial pig breeds including Duroc, Landrace and Large White had close relationship with each other, they also, to some extent, displayed genetic differentiation. Nanchang White pig and Large White, L95 dam line from PIC and Meishan pig had intimate genetic relationships with each other, which were consistent with its breeding history. Moreover, the cluster results of many other Chinese native pig breeds, including Meishan, Jiaxing Black, Guanchao, Tengtian Spotted, Shangyou Spotted and Wanan Spotted, were consistent with morphology, geographical distribution and exiting classification. It was concluded that AFLP provided a valuable tool for assaying genetic diversity and population genetic relationships in farm animals.