Increased infestation of weedy rice—a noxious agricultural pest has caused significant reduction of grain yield of cultivated rice (Oryza sativa) worldwide. Knowledge on genetic diversity and structure of weedy rice populations will facilitate the design of effective methods to control this weed by tracing its origins and dispersal patterns in a given region. To generate such knowledge, we studied genetic diversity and structure of 21 weedy rice populations from Sri Lanka based on 23 selected microsatellite (SSR) loci. Results indicated an exceptionally high level of within-population genetic diversity (He = 0.62) and limited among-population differentiation (Fst = 0.17) for this predominantly self-pollinating weed. UPGMA analysis showed a loose genetic affinity of the weedy rice populations in relation to their geographical locations, and no obvious genetic structure among populations across the country. This phenomenon was associated with the considerable amount of gene flow between populations. Limited admixture from STRUCTURE analyses suggested a very low level of hybridization (pollen-mediated gene flow) between populations. The abundant within-population genetic diversity coupled with limited population genetic structure and differentiation is likely caused by the considerable seed-mediated gene flow of weedy rice along with the long-distance exchange of farmer-saved rice seeds between weedy-rice contaminated regions in Sri Lanka. In addition to other effective weed management strategies, promoting the application of certified rice seeds with no weedy rice contamination should be the immediate action to significantly reduce the proliferation and infestation of this weed in rice ecosystems in countries with similar rice farming styles as in Sri Lanka.

Weedy rice (Oryza sativa f. spontanea) is a notorious weed that infests paddy fields worldwide. Understanding the morphological variation pattern of this weed in a given rice‐planting region will facilitate its effective management and use. Here, 29 populations, covering nearly all the rice‐cultivation regions in Sri Lanka, were characterized in a common‐garden cultivation experiment that was based on 13 morphological traits. The variation level of the weedy rice populations was considerably high, as estimated by the Simpson and Shannon–Weaver indices. An ANOVA revealed a higher level of among‐population variation than within‐population variation. Seed shattering was the most variable trait and the seed length and width were the least variable traits, as indicated by their coefficient of variation. The results of the principal component analysis, in which the first two principal components represented 57.5% of the total variation, indicated the important role of such traits as plant height, seed weight and number of tillers and panicles in the divergence of the weedy rice populations. However, the variation was not associated with their geographical locality. Knowledge of such a morphological variation pattern provides opportunities to design strategic management methods for weedy rice control in Sri Lanka, in addition to the proper use of it as a genetic resource for rice improvement.