Through polymorphism analysis of genes associated with hindquarters development on chromosome 18 in Xinjiang meat sheep, we sought genes that are associated with increased hindquarters musculature in the hope to provide theoretical guidance to molecular marker-assisted selection of meat sheep. The polymorphism of Callipyge (CLPG) gene was analyzed by PCR-SSCP and PCR-RFLP in populations of Dorset and Suffolk breeds and their F1 and F2 crosses with local Xinjiang Fine Wool sheep. Results showed that there was no PCR-RFLP polymorphism at 103849 bp in the region between DLK1 and GTL2 on chromosome 18, which suggested that hindquarters over-development was not controlled by the callipyge gene (CLPG) in Xinjiang meat sheep group. In addition, single nucleotide polymorphisms (SNPs) were detected at the Meg3.9 locus on chromosome 18 by PCR-SSCP. Based on the polymorphism, three genotypes AA, AB and AC could be discerned in this locus, with AA being the major one. The relationship between the genotypes and hindquarters hypertrophy was also investigated in the same group. Results indicated that the AC genotype had a significant impact on the hindquarters hypertrophy while the other two were not related to the muscling trait. In F1 crosses between Dorset and local fine wool sheep breeds, there was a significant difference in carcass weight and slaughter rate between the AC genotype and the other two genotypes (P<0.05), but there was not significant difference in the monthly live weight among the three genotypes (P<0.05). Based on the above, we found the muscling trait did not result from the mutation in at the 9571-268.3 site of the CLPG locus. Thus it may be under the influence of other genes or multiple linked QTL.