Abstract: The polymorphisms of estrogen receptor (ESR) and follicular-stimulating hormone beta subunit (FSHβ) genes were detected by DNA sequencing and PCR-SSCP methods, and effects of combined genotypes of ESR and FSHβ loci on reproductive traits in pigs were analyzed by the least square analysis. Data of total number born (TNB) and number born alive (NBA) from 323 sows, including five Shandong native pig breeds and three western pig breeds, were collected. The results showed that the polymorphic sites of both ESR and FSHβ genes were found in all populations tested. The combined genotypes distribution, however, revealed great differences between Shandong native pig breeds and western pig breeds. It was demonstrated that the effects of combined genotypes on TNB and NBA were significant (P<0.05). The sows with combined genotype BBBB are the most prolific. For the first and later parities sows, BBBB combined genotype produced 2.54 TNB, 2.65 NBA and 2.29 TNB, 2.35 NBA more than AAAA combined genotype, respectively. Moreover, the genetic effects of combined genotypes on litter size traits were not the simple summation of the isolated genotypes.