By using rice SSRP,RAPD and AFLP molecular markers,the genome of rice transgenic line “Minghui 63 Xa21” was analyzed.32 SSRP primers,42 RAPD primers and 8 AFLP primers could produce obvious PCR bands in the analysis of at least 12 individual plants selected randomly from “Minghui 63 Xa21” T 3 generation.Totally 550 PCR bands,equivalent to 550 genomic sites,were detected.Different individual plants of the transgenic homozygous line displayed almost the same PCR pattern.Compared with the control “Minghui 63”,no difference was found in their PCR patterns.This indicated that the introduction of Xa21 into the genome of “Minghui 63” did not change these 550 genome sites and their heredity.Very few variant PCR bands were observed in some individual plants from both “Minghui 63 Xa21” and “Minghui 63”.However,the variant percentage was equivalent between the transgenic line and the non-transgenic control line.