Abstract: Eight microsatellite loci which in 2nd and 5th chromosome were selected according to the genetic map of male goat and related reports.The population including 250 pure Boer goats in this study.The results showed that, for the BMS1248, BMS1898, ILSTS034, LSCV22, LSCV37, OarFCB011, IDVGA64, INRA040, the number of effect alleles(Ne), heterozygosity (H) and polymorphism information content (PIC) in the Boer goats population were 10.057 6，0.900 6，0.892 0； 6.831 5，0.853 6，0.839 6； 8.101 8，0.876 6，0.864 0； 7.067 5，0.858 5，0.841 7； 7.730 7，0.870 6，0.857 3；5.912 5，0.830 9，0.810 1；6.134 7，0.837 2，0.817 2；5.957 8，0.832 2，0.812 2， respectively. The relating effects between markers and growth traits were analyzed in a generalized linear model, the results indicated that the 162/140 genotype of BMS1248 had positive significant effect on birth weight, birth length, birth height, birth chest; 119/101 genotype of BMS1898 had positive significant effect on birth weight, birth length, birth height, 111/111 genotype had positive significant effect on birth chest; 193/167 genetype of ILSTS034 had positive significant effect on birth weight,while 193/167 and 199/167 had positive significant effect on birth chest; 161/147 and 159/143 genotype of LSCV37 had negative significant effect on birth weight, while 161/147 genotype had negative significant effect on birth weight and birth length; 281/243 genotype of IDVGA64 had negative significant effect on birth weight and birth length; 246/216 genotype of INRA040 had positive significant effect on body weight and birth chest,while 246/216 and 238/238 had positive significant effect on birth height.