genetic diversity and structure in 316 accessions of rice germplasm from ASEAN was assessed using 72 pairs SSR markers. A total of 387alleles were detected ranging from2 to 12 per locus with the mean of 5.38, and there are 111 rare alleles in frequency <5%, accounting for 28.7%.of all alleles. The Nei’s gene diversity indices(He)ranged from0.055 to 0.855,wieh the average of 0.623. the He of rice germplasms in the Philippines was the highest, the followings were in Vietnam(He=0.515)> in Laos(He=0.467)>in Cambodia(He=0.455).The analysis of molecular variance(AMOVA) indicated that genetic variation came from between different geographical groups, and between different groups with significant difference at 0.001 probability level.Neighbor-joining trees bases on Nei’s 1973 genetic distance showed 316 rice germplasm could be distinguished as indica and japonica, but not be classified better into groups according to geographical regions. The result of population structures analysis indicated that will have a relatively obvious genetic structure when k=2. The secondly is K=5,it showed that Philippines population is divided into 3 small distinct groups which obvious genetic differentiation structure, The present study verified that rice germplasm from ASEAN have rich genetic diversity and structure which is an excellent basis for rice breeding.in selecting parents.