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Abstract While the positive relationship between plant diversity and ecosystem functioning is frequently observed and often attributed to direct plant–plant interactions, it remains unclear whether and how the effects of plant diversity endure through soil legacy effects, particularly at the level of genotypic diversity. We manipulated the genotypic diversity ofScirpus mariqueterand tested its soil legacy effects on a conspecific phytometer under low‐ and high‐water availability conditions. We found that genotypic diversity enhanced phytometer productivity through soil legacies, with stronger effects under low‐water availability conditions, improving its resistance to water stress. Moreover, this effect was attributed to the association between asexual and sexual reproductive strategies by increasing ramet number to ensure plant survival under low‐water availability and promoting sexual reproduction to escape stress. The observed diversity effects were primarily associated with increased levels of microbial biomass in soils trained by populations with diverse genotypes. Our findings highlight the importance of plant genotypic diversity in modulating ecosystem functioning through soil legacies and call for management measures that promote genetic diversity to make ecosystems sustainable in the face of climate change.