Weedy rice (Oryza sativa f. spontanea) is one of the most notorious weeds occurring in the rice fields of Thailand and Laos. Genomic research can be applied to improve understanding of weedy rice biology. The purpose of this study was to evaluate the genetic diversity of a collection of weedy rice from Thailand and Laos. Ninety-nine weedy rice accessions from four populations were evaluated by means of four SSR markers. A total of 49 alleles were detected. The number of alleles per locus ranged from 3.6 to 8.7, with an average of 7.6. The overall genetic diversity of weedy rice populations was relative high (H_s=0.619). The genetic differentiation among the four populations showed that genetic variability mainly existed among weedy rice individuals rather than among populations in all four populations. Results from the present study are presenting a clearer understanding of the genetic diversity of weedy rice in Thailand and Laos.