Abstract: According to comparative genomics, four microsatellite loci including OarAE101, OarHH55, BM1329 and BMS2508 that linked to the fecundity gene FecB in the sheep chromosome 6 were analyzed for polymorphisms in Boer goat and Xinong Shaanen goat. The results indicate that there are genetic polymorphisms at these 4 microsatellite loci. The polymorphism information content (PIC) and number of effective alleles (Ne) are 0.834 0，0.722 2，0.820 1，0.685 5 and 6.719，4.098，5.610，3.542 respectively in Boer goats; the PIC and Ne are 0.765 5，0.738 7，0.670 1，0.682 0 and 4.849，4.360，3.520，3.609， respectively in Xinong Shaanen goats. The result of the effect of the 4 microsatellite loci on the litter size of 2 goat breeds showed that the allele 126 bp at OarAE101 has positive effects on the litter size in Boer goat but 134 bp has negative effects; the allele 120 bp and 124 bp at OarHH55 have positive effects on the litter size in Boer goat, but 130 bp/140 bp has negative effects; the allele 185 bp at BM1329 has positive effects on the litter size in Boer goat but 176 bp, 215 bp/240 bp have negative effects; the allele 118 bp at BMS2508 has positive effects on the litter size in Boer goat and 122 bp/141 bp, 148 bp has negative effects; the allele 108 bp, 114 bp/126 bp at OarAE101 have positive effects on the litter size in Xinong Shaanen goat and 124 bp has negative effects; the allele 120 bp at OarHH55 has positive effects on the litter size in Xinong Shaanen goat and 150 bp/165 bp has negative effects; the allele 185 bp at BM1329 has positive effects on the litter size in Xinong Shaanen goat and 176 bp, 215 bp/140 bp have negative effects; the allele 118 bp at BMS2508 has positive effects on the litter size in Xinong Shaanen goat and 141 bp, 153 bp/160 bp have negative effects.