A genetic linkage map comprising 148 SSR markers loci was constructed using an F2 population consisting of 90 lines derived from a sub-specific cross between a japonica variety Nipponbare and an indica variety Guangluai-4. The F2 population showed high significantly distorted segregations. Among these SSR markers, 49 markers(33.11%) showed the genetics distortion(P<0.05). Of them, 36 markers deviated toward male parent indica GuangLuAi-4 and 13 markers toward heterozygote, but none toward the female parent Nipponbare. It was found that the segregation distortion might be caused by gametophyte and zygote. Since most gametophyte loci and sterility loci were mapped in segregation distortion regions, it indicated that the segregation distortion may be caused by these gametophyte loci and sterility loci. Finally, this research also analyzed the skewed segregation of some markers, which had not been mapped on chromosome.