Technical Abstract: Plant leaves host a specific set of microbial epiphytes. These phyllosphere organisms form a large community, with annual crops alone covering millions of hectares each year. Host plant genetic factors and abiotic stresses such as UV-B are key in shaping patterns of epiphyte diversity; we analyzed the genetic architecture of Zea mays host control. • Bacterial rDNA diversity was measured with molecular methods in a maize recombinant inbred mapping population with and without ultraviolet-B radiation, and in a factorial experiment to test for genetic correlation between host-plant pathogen resistance and phyllosphere diversity. • Thirteen UV-B-specific loci and ten loci with an environment-independent genetic effect on bacterial diversity were found. Several of the UV-B-specific loci co-occurred with loci involved in fungal leaf blight resistance in the field. A factorial experimental design was used to test the effects of antibiotic treatment and blight-resistant genotype on bacterial diversity; the resistant genotype had less beta diversity under control no-antibiotic conditions. • The coincidence in chromosomal locations that control bacterial diversity with locations that control fungal pathogen resistance suggests two possible mechanistic models: first, that leaf attractiveness leads to diverse bacterial epiphytes and facilitates rapid fungal pathogen spread, or that, alternatively, pathogen susceptibility is due to loss of a suppressive bacterial species. The antibiotic treatment results support the second model.