Abstract: The aim of this research was to understand the population genetic variation and relationship, genetic differentiation between populations. In this study, 4 SNPs were identified in the porcine Solute Carrier Family 6 Member 14（SLC6A14）by directly sequencing DNA pools from 19 founder animals（2 White Duroc boars and 17 Erhualian sows）of a White Duroc × Erhualian resource population. The three mutation sites（c.1438G>A, g.7944A>T, g.21063G>T）were chosen and used for detecting the polymorphism in 11 pig breeds by PCRRFLP method. The results showed that 11 pig breeds presented varation at the g.7944A>T and g.21063G>T sites in the SLC6A14. Moreover Huai and Erhualian pigs have dominant varation at g.7944A>T site in the SLC6A14（0.01<P<0.05）, while Licha Black, Huai,Yushan Black, Hezuo Tibet, Bamei pigs also have significant varation at g.21063G>T site in the SLC6A14（P<0.01）, AT was dominant genotype. No variation was detected in the European pig populations (Landrace, Large White and Duroc). only GG genotype was presented. Whereas variation was presented at the c.1438G>A site of 8 Chinese native pig breeds. The genetic distance of 11 pig populations were calculated from 3 sites polymorphism data. The cluster tree was constructed by UPMGA method. The results showed that Chinese local pig populations had distinct genetic differentiation with exotic pig populations. It was concluded that Chinese indigenous pig breeds have higher genetic variation and diversity than the exotic pig breeds at the three SNPs, genetic differentiation existed between Chinese pig populations and exotic breeds. The majority of pig breeds were consistent with the geographical distribution and breed characteristic.