Progression to homozygosity of heterozygous genotypes was studied in a cross of the rice subspecies Pei'ai64s and Nipponbare, using a set of 157 polymorphic microsatellite (SSR) markers. The segregation of heterozygous genotypes ranged from 49.13% in the F(2) population to 4.52% in the F(6) population (progression value 11.15%). The heterozygous genotypes were widely distributed in 180 F(2) plants, 330 F(6) lines, and 157 SSR markers. Homozygosity progression showed a wide distribution in plants and SSR markers but not in chromosomes. The segregation of heterozygous genotypes was not significant between populations but varied greatly in F(2) plants, F(6) lines, and SSR markers. The correlation between the progression to homozygosity and the heterozygosity of SSR markers was significant at the chromosome level. The segregation of heterozygous genotypes in plants, SSR markers, and chromosomes was not completely in accordance with Mendel's law. This information will help rice geneticists and breeders to understand heterozygous genotype segregation at the DNA level and to screen special markers for breeding.