Glyphosate-resistant (GR) cropping systems are popular and used extensively by producers. However, the long-term impacts of heavy reliance of this technology on weed community structure are not known. Five fully phased field experiments (two no-tillage and three conventional tillage) were established at four locations in southwestern Ontario where the effects of herbicide system (glyphosate or conventional) in corn and soybean and crop rotation (corn–soybean or corn–soybean–winter wheat) on midseason weed communities were examined. Multivariate analysis on data over the last 3 yr of the 6-yr experiment showed that weed communities were distinctly different among the treatments within each experiment. At several locations, midseason weed communities were more similar in corn and soybean treated with glyphosate compared to the same crops treated with conventional herbicides, reflecting the continuous application of the same selection pressure in both crops. Analysis of trait-densities revealed an increase in species with late initiation of seedling recruitment at the expense of weed species with medium time of initiation of seedling recruitment rather than early recruiting species. Increases in perennial species, species with a short interval between recruitment and anthesis, and wind-dispersed species were also observed. Trait-density–based analysis of the weed community was an effective method for reducing the complexity of divergent weed communities that enabled direct quantitative comparison of the herbicide-induced effects on these weed communities.