Abstract: Karyotype analysis was carried out by means of culturing whole peripheral blood from 394 pigs, which were produced from three hybridization combinations of 13/17 Robertsonian translocation pig. According to karyotype all the pigs were divided into different groups. A RsaⅠrestriction enzyme polymorphic site (locus A) in a 1746 bp fragment of porcine POU1F1 gene was detected by using PCRRFLP analysis and a mutation (locus E) in intron 5 of porcine POU1F1 gene was found by using PCRSSCP analysis in three hybrid populations. At the same time, the effects on growth traits and carcass traits of POU1F1 gene were estimated according to their growth and slaughter data. The result of population genetics analyses demonstrated a significant effect on growth in locus A and a significant association with growth and loin eye area for locus E(P<0.05). The results indicated that growth and loin eye area were correlated with polymorphisms of POU1F1gene which could be used as an interpretation for genetic mechanism on heterozygous advantage of Robertsonian translocation at the molecular level.