Simple SummaryTo generate knowledge on how human activities influence plant evolution in agroecosystems, we analyzed allelic introgression fromjaponicarice varieties into theindicatype of weedy rice, and the impact of crop-to-weed introgression on the genetic differentiation and diversity of the weedy populations in Jiangsu Province of China, based on InDel (insertion/deletion) and SSR (simple sequence repeat) molecular fingerprints. Results from these analyses indicated a positive correlation between increased introgression fromjaponicarice varieties and genetic differentiation in weedy rice. In addition, increased crop-to-weed introgression formed a parabola pattern of dynamic genetic diversity in weedy rice. Our case study indicated that human activities such as the frequent change in crop varieties can influence the evolution of their conspecific weeds through crop-to-weed introgression, which promotes their genetic differentiation and dynamics of genetic diversity in agroecosystems.AbstractAs an important driving force, introgression plays an essential role in shaping the evolution of plant species. However, knowledge concerning how introgression affects plant evolution in agroecosystems with strong human influences is still limited. To generate such knowledge, we used InDel (insertion/deletion) molecular fingerprints to determine the level of introgression fromjaponicarice cultivars into theindicatype of weedy rice. We also analyzed the impact of crop-to-weed introgression on the genetic differentiation and diversity of weedy rice, using InDel (insertion/deletion) and SSR (simple sequence repeat) molecular fingerprints. Results based on the STRUCTURE analysis indicated an evident admixture of some weedy rice samples withindicaandjaponicacomponents, suggesting different levels of introgression fromjaponicarice cultivars to theindicatype of weedy rice. The principal coordinate analyses indicatedindica–japonicagenetic differentiation among weedy rice samples, which was positively correlated with the introgression ofjaponica-specific alleles from the rice cultivars. In addition, increased crop-to-weed introgression formed a parabola pattern of dynamic genetic diversity in weedy rice. Our findings based on this case study provide evidence that human activities, such as the frequent change in crop varieties, can strongly influence weed evolution by altering genetic differentiation and genetic diversity through crop–weed introgression in agroecosystems.