AbstractWeedy rice (Oryza sativa f. spontanea) is a conspecific weedy relative of cultivated Asian rice (O. sativa L.) that occurs in paddy fields worldwide. The mechanism underlying the persistence of weedy rice in rice fields remains unclear. We tested for evidence that southern Chinese weedy rice has originated through pollen flow from weedy rice that has resulted in hybridization with three‐line hybrid rice cultivars, which have been extensively cultivated in southern China for the last 40 yr and now account for over half the total rice cultivation in China. To test the hypothesis, we screened for the presence of the maternally inherited WA352 gene in weedy rice populations in southern China. WA352 is a mitochondrial gene that controls wild abortive cytoplasmic male sterility (CMS‐WA) and is present in three‐line hybrid rice cultivars. Screening of 48 weedy rice populations (939 accessions) indicates that 36 of 48 populations (75%) and 325 of 939 accessions (34.6%) harbor the WA352 gene. The rate is significantly higher than the 1% outcrossing rate between weedy rice and rice cultivars. Further analysis indicates significance between the frequency of the WA352 gene in weedy rice populations and depth of plowing. Our results suggest that outcrossing with rice cultivars is one of the important mechanisms underlying the persistence of weedy rice in southern China and that deep plowing may be conducive to promoting the persistence of weedy rice derived from hybridization (three‐line hybrid rice × weedy rice).