Objective To understand the genetic background of the specific pathogen-free Yorkshire and Landrace pigs, imported from Canada by Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences. Methods The population genetics were investigated by using 19 pairs of microsatellite primers. Results In the Yorkshire pigs and Landrace pigs, 84 and 89 alleles, respectively, were detected at 19 microsatellites loci. The average polymorphic information content and mean heterozygosity in the Yorkshire pigs were 0.5271 and 0.5877, and in the Landrace population were 0.5652 and 0.6066, respectively. Because of the significant (P <0.01) differences of alleles in different loci such as S0155,S0143,S0178,Sw857 and Sw936, it made them possible to be used to identify Yorkshire and Landrace pigs' breed. F-statistics showed that the differentiation within the population was small and genetic structure was stable. Conclusions Compare with the domestic pedigree large White and Landrace pigs, the SPF pedigree pigs imported from Canada are more stable in genetic structure, and can be used as laboratory animal models in animal science research.