Abstract:SSR (simple sequence repeat) and AFLP (amplified fragment length polymorphism) are PCR-based molecular markers developed in recent years. In this study, the authors analyzed the polymorphisms, inheritance and distribution of SSR and AFLP markers using an F2 population from a cross between cultivar "Aijiao Nante" ( Oryza sativa L. ssp. indica) and an accession of the common wild rice ( O. rufipogon Griff). A total of 200 new markers were obtained including 28 SSR and 172 AFLP markers. Six of the 28 SSR markers were developed by National Key Laboratory of Crop Genetic Improvement (NKLCGI) using DNA sequences from GenBank and the other 22 were from data published previously. The 172 AFLP markers were from a total 228 polymorphic bands amplified using 25 selected primer combinations. Mapping of the 200 new markers using NKLCGI‘ S previously developed RFLP map based on the same F2 population resolved these markers to all 12 rice chromosomes. Integration of the SSR and AFLP markers into the RFLP map resulted in a high density molecular linkage map containing 612 polymorphic loci.