Several weedy red rice populations have evolved resistance to imidazolinoneherbicides worldwide. The understanding of the factors related to theherbicide resistance in weedy red rice is important to prevent itsoccurrence in new areas where imidazolinone-resistant rice cultivars arebeing used, and to manage the new rice cultivars resistant to herbicideswith modes of action other than the acetolactate synthase (ALS)-inhibitorsthat are being developed. The objectives of this study were to analyze therelationship of weedy red rice populations from southern Brazil with ricecultivars and wild Oryza species and to evaluate theoccurrence of introgression from rice cultivars and seed migration as theorigin of resistance to imidazolinone herbicides in weedy rice. The studywas based on 27 weedy red rice populations, seven rice cultivars, and fourwild Oryza species that were genotyped with 24 simplesequence repeats and three ALS-specific single-nucleotidepolymorphism markers. A large proportion of the genetic variation of theweedy red rice populations was found within (74%) rather than amongpopulations (26%). The weedy red rice populations were more closely relatedto the newer rice cultivars that are imidazolinone-resistant than to theolder cultivars. The South American native Oryza glumaepatula and the other wild Oryza species—Oryza rufipogon, Oryza longistaminata, and Oryza glaberrima—clustered separately from weedy redrice populations, indicating a low likelihood of introgression among weedyred rice and these wild species. Seed migration was an important factor inthe genetic structure of the evaluated weedy red rice populations, althoughgene flow by pollen from resistant cultivars was the principal reason forthe spread of herbicide resistance.