Abstract The melanocortin-4 receptor (MC4R) is a G-protein coupled receptor superfamily member, which has been implicated in regulating food intake, energy balance and body weight in mammals. Though the mutations of MC4R have been identified as genetic markers for growth traits in many livestock species, little is known about sheep MC4R gene. In this study, MC4R gene was amplified and sequenced to screen single nucleotide polymorphism sites (SNPs) and three novel SNPs (g.306 G>A and g.706 C>A in the coding region and g.1267 G>A in the 3′-UTR) were detected. The genetic structure of the three SNPs were examined by PCR-RFLP and CRS-PCR-RFLP, respectively, in 298 individuals of two sheep populations (Hu sheep, Hu; East Friesian × Hu crossbred sheep, EH). Association analysis between three SNPs and body traits revealed that two of the SNPs were associated with body weight, except for g.306 G>A mutation; and all three loci were significantly associated with body size. Haplotype blocks showed that there were none loci linked within Hu nor EH MC4R gene, but both generated principally seven haplotypes. Moreover, H1H3 (GA-CC-GA) diplotype had better performance than other diplotypes in Hu sheep ( P P > 0.05). These preliminary results indicate that three novel MC4R SNPs are related to the growth development, which may be used as genetic markers for sheep breeding and potentially afford a good foundation for further study on MC4R gene.