Five microsatellite markers BM1329, BM143, OarHH55, TGLA68, and LSCV043, which were closely linked to the fecundity gene FecB and FecX in ovis aries sheep, were chosen based on their high conservatism in the close species and another 4 microsatellite markers ETH225, INRA063, BM1225, and MAF0214 were selected to analyze their correlation with the litter size of Boer goat. All the 9 microsatellite loci in Boer goat were high polymorphism locus (PIC > 0.5). Twelve alleles were found to be significantly correlate with litter size of Boer goat. Three of them, i.e., 120 bp and 108 bp of BM143, 183 bp of ETH225, were positively correlated to first parity litter size of Boer goat. Eight alleles, i.e., 216 bp of BM1329, 110 bp of BM143, 255 bp and 239 bp of BM1225, 175 bp, 177 bp and 189 bp of INRA063, and 163 bp of ETH225, had negative correlation with first parity litter size. One allele, i.e., 115 bp of TGLA68, were positively correlated to second parity litter size.