Abstract: Genetic diversity was analyzed among 15 main male sterile lines of indica hybrid rice from China with 99 pairs of SSR marker evenly distributed in the 12 chromosomes of rice.The results indicated that 71(71.1%) pairs of SSR marker showed polymorphism.There were 171 alleles detected with those 71 pairs of SSR marker.The number of alleles for per locus ranged 2-5 with an average of 2.47.The average of He was 0.716 and average of PIC was 0.393.The 15 main male sterile lines were divided into two groups at genetic distance 0.693.The sterile line Guangzhan 63S could be grouped alone.Another group was composed of four photo-thermo-sensitive genic male sterile lines and all main three-line male sterile lines.The clustering results based on SSR analysis was basically consistent with the pedigree of 15 main male sterile lines.