Abstract: In order to analyze the genetic contribution of the ancestors to the offsprings from rice subspecies cross, 16 parents and 39 varieties derived from special germplasm (92gk729) were analyzed by 221 pairs of SSR primers and pedigree allele method.The results showed that: (1) In 92gk729, the special fragment of the recombination of the four ancestors were amplified with 10 pairs of SSR primers;5specific sites of the recombination could stably transmit into the offsprings;one specific site of the recombination did not appear at the ancestors and the offsprings, so these special fragments need to be further analyzed. (2) The genetic contribution ratio of Ketan Nangka, JiaNanJing, 02428 and Minghui72to 92gk729 was 15.09%, 21.32%, 22.78% and 34.64%, respectively.The hybridization and recombination of the chromosome segment of the four parents amplified new specific sites, whose genetic contribution rate was 6.17%. (3) On every chromosome, the trend of the genetic contribution from the four ancestors to the offsprings was gradually decreased, accompanied with the increase of generations.The genetic contribution from the four ancestors to the offsprings showed Minghui72>02428>JiaNanJing>Kenta Nangka. (4) The cluster analysis of the data gained by the pedigree allele method was performed.The results showed that of the same hybrid combination, most of the varieties of the same genealogical branch with the derivative relations could be clustered together;the material of high derivative generations in close sibship of descendant could be clustered together.We could conclude that pedigree allele method could better reflect the genetic contribution of the ancestors to the offsprings.