Single nucleotide polymorphisms (SNPs) of hircine myf-5, myf-6 genes and 5′flanking region of the myoD gene (myoD 5′) were analyzed by PCR-SSCP in Boer goat and Xuhuai white goat. Three genotypes were found at the myf-5 locus of Xuhuai white goat, denoted AA, AB and BB, while all of Boer goats were of AA genotype. Only AA and AB genotypes were found at myf-6 and myoD 5′ loci. The effects of genotypes of myf-5, myf-6 and myoD 5′flanking region loci on body measurement traits were estimated. The results showed that genotypes at the myf-5 locus were significantly associated with hucklebone width and hucklebone width index in Xuhuai white goat (P<0.05). Genotypes at the myf-6 locus were significantly associated with withers heights and hucklebone width index in Boer goat (P<0.05), but no significant associations were found for any traits in Xuhuai white goat. The myoD 5′ locus was not significantly associated with any traits in both types of goat.