Abstract: The Alu insertion sequence of the porcine FSHβ and GDF9 genes were obtained using the PCR(Polymerase chain reaction) technique, from Liaoning Black，Landrace，Large White，Danyu Black and Duroc pigs, and the polymorphism was investigated，and the sequence was analyzed by bioinformatics in this study. The GLM model was constructed to study the relationship between litter size and the polymorphism of the Alu. The result showed that litter size of individuals with dominant genotype BBDD were 15 more than that with genotype AACC（P<0.01）. Otherwise, the FSHβ and GDF9 genes were correlated deeply to the major gene influencing on the litter size, which may be considered as a genetic marker associating with pig litter size. The dominant genotype (BBDD) can improve the litter size traits.