Drought stress in crops affects belowground fungal microbiomes. Our work shows that fungal community structure is driven by watering levels and plant genotypes. Our analyses demonstrate that the abundance of plant pathogens and arbuscular mycorrhizal fungi increases with crop genetic variation levels. This work provides evidence for drought and genetic drivers of belowground sunflower-fungi interactions and offers a framework for leveraging these interactions to further understand how microbiome community structure can improve plant productivity under stress.