Weedy (red) rice is a major pest of cultivated rice in the United States (U.S.) and worldwide, causing decreases in both yield and market value. Previous work has shown that U.S. weedy is comprised of two genotypically distinct lineages that are strongly correlated with strawhull awnless (SH) and blackhull awned (BHA) morphologies. Each of these lineages has arisen independently, and is most closely related to a specific variety of Asian cultivated rice (indica and aus respectively) (Reagon et al. 2010). Here we resequence the entire genome of one SH, one indica, one BHA and one aus individual and assess genome-wide levels and pattern of variation between weedy and cultivated forms of rice. Genome-wide patterns of divergence will be combined with QTL mapping to identify candidate genes affecting weedy traits. Together, these analyses will allow us to make inferences regarding the processes affecting the evolution of weediness in a parallel system.