The segregation ratio of markers in an F2 population derived from Rudongjijiaoyaguo (Rdjjyg) and Zhongmian971 (Zm971) was studied using 3 morphological markers, 20 SSR markers, and 11 SRAP markers. Totally, 24 markers (77.42%) showed a distorted segregation and all of them skewed toward the female genotype, which was peculiar in recent cotton research. All the three types of SSR markers and SRAP marker showed distorted segregation, but the morphological markers (Purple stem, Okra leaf, and Red spot color) were normally segregated. this indicated that such a novel segregation distortion phenomenon resulted from interior genetic factors. The allele frequency and the distribution of different genotype frequencies in the F2 population were analyzed in codominant markers, to find out factors attributed to distorted segregation. Most of them implied distorted allele frequency, but it was normal genotype frequency, which showed that these markers were influenced at the gamete level.