Northeastern Thailand and Laos are the two most important habitats of the wild, (Oryza rufipogon). To examine the genetic diversity of this wild rice species, seven rice microsatellite markers were used to evaluate the genetic diversity of 94 accessions. In the entire sample a total of 83 alleles were detected, with an average of 11.85 allele per locus. The total gene diversity was an average of 0.733. The Laos population showed higher measures of genetic diversity (i.e., mean of allele number per locus, mean of genetic diversity, and mean of PIC value) than the northeastern Thailand population. Clustering analysis, using STRUCTURE to determine the true number of populations (k), reveals occurrences of different gene pools of wild rice among the examined populations. This observation support the hypothesis of the presence of subgroups in wild rice from northeastern Thailand and Laos.