Abstract: Cluster analysis of 24 indica rice varieties（lines）by 4 different SSR primers using NTSYS，DPS and MAGE software were implemented in this study. The results showed that three groups including restorer lines， cytoplasmic male sterile lines and short photoperiod sensitive sterile lines were distinguished no matter using NTSYS software by the similarity factor，or using DPS and MAGE software clustering analysis based on genetic distance，the results of clustering analysis were different with the number of markers and alleles，especially the sub group under the male sterile lines and restorer lines，which were recognized as dominant group of rice. This study suggests that the number of alleles detected by molecular markers affects the accuracy of clustering results and the effective construction of rice heterosis groups.