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Negative plant-soil feedbacks can serve as a mechanism for plant species coexistence. Despite predicted changes in precipitation patterns due to climate change, little is known as to how the strength and direction of feedbacks change under differing soil moisture regimes. We performed a fully reciprocal greenhouse experiment where seedlings of two co-occurring Asclepias spp. (milkweed) were grown either with their own or the other species' microbial communities under high or low watering treatments. We found that seedlings of each species were smaller when exposed to conspecific relative to heterospecific soil biota, perhaps due to a build-up of specific soil pathogens. Importantly, this negative feedback diminished under reduced water-availability, and also in the absence of live soil organisms. Our findings suggest that the ability for plants to coexist may be fundamentally altered in areas that face increased drought.