Cover crops are plants grown to provide regulating, supporting, and cultural ecosystem services in managed environments. In agricultural systems, weed suppression services from cover crops can be an important tool to promote sustainability as reliance on herbicides and tillage for weed management has caused pollution, biodiversity loss, and human health issues. However, to effectively use weed suppression services from cover crops, farmers must carefully select species that fit within their rotations and suppress their problematic weeds. Understanding how the relatedness between cover crops and weeds affects their interactions will help farmers select cover crops for targeted weed management. The phylogenetic distance between species reflects their relatedness and was studied through a series of field experiments that compared weed suppression in winter and summer cover crops with tilled controls. This study demonstrates that cover crops can reduce up to 99% of weed biomass and alter weed community structure by suppressing phylogenetically related weed species. Results also suggest that cover crop planting season can influence weed community structure since only overwintering treatments affected the phylogenetic distance of weed communities. In an applied context, these results help develop cover crop-based weed management systems, demonstrating that problematic weeds can be managed by selecting phylogenetically related cover crop species. More broadly, this study provides a framework for evaluating weed communities through a phylogenetic perspective, which provides new insight into plant interactions in agriculture.