Plant genetic variation plays an important role in structuring root-associated mycorrhizal communities, but how this variation is partitioned within plant species is currently unknown. This research utilizes switchgrass genetic resources to identify the drivers of mycorrhizal community assembly within a plant species and to elucidate the plant genetic architecture of mycorrhizal community traits. We use fifteen replicated genotypes to identify variation in community assembly within and among switchgrass genotypes and to test whether mycorrhizal community assembly is phylogenetically conserved or associated with physiological trait adaptations. We use a larger, unreplicated selection of more than 600 tetraploid switchgrass genotypes to identify genes and gene regions that are associated with mycorrhizal community composition. We also use this large dataset to assess differences between subpopulations and ecotypes, to determine whether community composition is associated with other plant physiological traits that have also been measured in the switchgrass, to identify colocalized genes across the switchgrass species, and to assess the heritability of mycorrhizal community assembly. Finally, we compare the mycorrhizal community assembly of roots from tetraploid switchgrass individuals to octoploid switchgrass individuals grown in the same common garden to characterize the effect of genome duplication on mycorrhizal community composition. This data provides some insight into how mycorrhizal community assembly is affected by plant genotype and may potentially be a trait under selection. The results of this study provide valuable insights into the genetic architecture of plant-mycorrhizal interactions in switchgrass.