Thailand's northeast (NE) region is an area of high-quality cultivated rice (Oryza sativa L.) production. However, an outbreak of weedy rice has recently spread throughout the region. Weedy rice is phenotypically and morphologically similar to cultivated rice, making identification difficult. The prospective management of weedy rice in the future will involve the study of its genetic diversity and population structure in this region. This study assesses the genetic diversity and population structure of 380 weedy rice samples in the northeast of Thailand through simple sequence repeat (SSR) markers. Thirty-one SSR markers generated 213 alleles with an average of 6.87 per locus and an overall genetic diversity of 0.723. Based on its geographic origin, weedy rice in the Southern NE are showed greater genetic diversity than that in the Central NE and Northern NE areas. The outcrossing rate in all regions was relatively high, with the highest being in the Southern NE at 9.769%. According to genetic distance analysis, the clustering of weedy rice samples in northeast Thailand was not associated with the geographic region. Neighbor-joining and principal coordinate analysis revealed that the 380 weedy rice samples fell into two major clusters. Cluster I contained three weedy rice samples and four wild. In Cluster II, 377 weedy rice samples were closely related to the four cultivated rice cultivars as well as brownbeard rice (Oryza rufipogon Griffiths) wild species. The results suggest that weedy rice in northeast Thailand may have originated as a cross between cultivated and wild rice, as seen in the closely related species, O. rufipogon. Overall, the findings of this study demonstrate the high genetic diversity of weedy rice in this region. Notably, some samples adapted, performing more like cultivated rice, which may be problematic for the future production of high-quality rice in this region. The prevention of weedy rice should, therefore, be given greater consideration in future studies.