¹College of Animal Science and Technology, Shihezi University, Shihezi 832003, CHINA DOI : 10.9775/kvfd.2018.20488 This work was carried out to analyze of effects of twelve microsatellite loci and genetic heterozygosity on wool fineness and natural length, which are important indicators for evaluating of wool quality. 131 individuals from F2 and F3 generations of Australian Merino and Chinese Merino sheep (Xinjiang military reclamation type) mating were used as experimental subjects. Five loci on chromosome 1 and seven loci on chromosome 6 were determined as related with fineness and natural length of wool. The results showed that 3 loci significantly associated with wool fiber diameter (WFD), and 4 loci were significantly related to wool natural length (WNL). WFD increased by approximately 0.2%- 2.5%, and WNL decreased by 2%-10.93%, and also heterozygosity increased by 0.05 in the range of 0.5 to 1.0. These results could partially explain the molecular mechanism of heterosis for sheep wool quality. Provide theoretical support for the effective exploitation and utilization of this precious resource. Keywords : Wool fiber diameter, Wool natural length, Microsatellite, Heterozygosity, Sheep