Abstract: To reveal their genetic relationship on the molecular level of the major rice varieties and parental lines of hybrid rice in China, amplification of DNA from all 63 tested lines are successfully made using a set of 24 SSR (Simple sequence repeats) primer pairs located along 12 chromosomes in rice, with two pairs on each chromosomes, we detected a total of 135 alleles, whose number of per primer pairs ranged from 2 to 9, with an average 5.6, and FP（Polymorphisms frequency）values between 0.486-0.840, with an average of 0.682. Cluster analysis showed that indica subspecies include maintainer lines (lines that can maintain male sterile, group Ⅰ) and restorer lines (lines that can restorer male sterile, group II), which separately distributed in South China and the Changjiang River area, whereas Group Ⅲ corresponded to the japonica subspecies were also divided into two subgroups（GⅢ-1 and GⅢ-2）, which grown in North China and Jiangsu-Zhejiang provinces respectively. This indicated that geographic distribution is one of the major characteristics of rice varieties. The average genetic similarity of the indica varieties/lines (0.388) was significantly lower than that of japonica varieties (0.638), showing a higher level of genetic diversity of indica. Also restorer lines have a higher genetic diversity than maintainer lines. On the basis of the data we conclude that the genetic relationship constructed by SSR markers was identical and more accurate, compared with that by the pedigree analysis.

Key words: Rice (Oryza Sativa L.), Microsatellite marker, Genetic diversity, Genetic relationship