Word count (Total): 6693 Word count (Introduction): 818 Word count (Methods): 3241 Word count (Results): 1859 Word count (Discussion): 783 Number of figures: 6 (all in color) Number of tables: 1 Supporting Information: 4 tables + 7 figures (all in color) Word count (Acknowledgements): 105 Summary:• Macroorganisms' genotypes shape their phenotypes, which in turn shape the habitat available to potential microbial symbionts. This influence of host genotype on microbiome composition has been demonstrated in many systems; however, most previous studies have either compared unrelated genotypes or delved into molecular mechanisms. As a result, it is currently unclear whether the heritability of host-associated microbiomes follows similar patterns to the heritability of other complex traits. • We take a new approach to this question by comparing the microbiomes of diverse maize inbred lines and their F1 hybrid offspring, which we quantified in both rhizosphere and leaves of field-grown plants using 16S-v4 and ITS1 amplicon sequencing. • We show that inbred lines and hybrids differ consistently in composition of bacterial and fungal rhizosphere communities, as well as leaf-associated fungal communities. A wide range of microbiome features display heterosis within individual crosses, consistent with patterns for non-microbial maize phenotypes. For leaf microbiomes, these results were supported by the observation that broad-sense heritability in hybrids was substantially higher than narrow-sense heritability. • Our results support our hypothesis that at least some heterotic host traits affect microbiome composition in maize.