Background/Question/Methods Agricultural practices, such as crop rotation and planting cover crops, alter the composition of weed communities, likely because these agricultural practices alter the biotic and abiotic environmental conditions in ways that favor certain species over others. These differences in success among weed species likely result because certain suites of traits may be favored in different environments. For example, cover crops may increase light competition, so that only taller weed species can persist. We predict that the same forces contributing to differences in the population growth rates among species also will contribute to differences in fitness among genotypes within a species, and that the species traits favored at the community level (resulting in changing community composition) also may be favored intraspecifically (resulting in evolutionary change of focal populations). To test this hypothesis, we measured growth and physiological traits of all common weed species found in crop rotation and cover crop treatments at the Kellogg Biological Station LTER. Additionally, we measured these same traits and fitness on several thousand individuals of two focal species to estimate selection within each treatment. Results/Conclusions We observed strong selection for increased height on both Chenopodium album and Ambrosia artemisiifolia (p < 0.0001), and cover crop treatments increased the strength of selection on this trait in one of our focal species (C. album χ2=3.74, p = 0.05). However, we did not detect this trend at the community level (p > 0.5). We found that weed species responded differently to cover crop treatments (cover crop x species interaction on biomass, p < 0.02), and community composition differs across cover crop treatments. Crop rotation treatments had limited impacts on patterns of natural selection, but did alter weed species diversity (F1,15=53.36, p < 0.001), the relative abundance of individual species (p < 0.0001), and community composition. Interestingly, taller weed species were once again favored across all rotation treatments, but three year rotations increased the advantage of tall weed species compared to shorter weed species (F1,709=3.07, p=0.08). These findings suggest that agricultural practices are altering selection on weed traits, both at the community and population level but that the traits contributing to high fitness within populations may not necessarily be the same traits responsible for variation in the relative performance of different weed species.