The plant-associated microbiome has been shown to vary considerably between species and across environmental gradients. The effects of genomic variation on the microbiome within single species are less clearly understood, with results often confounded by the larger effects of climatic and edaphic variation. In this study, our objective was to confirm that maize genomic variation effects the rhizosphere bacterial communities in the absence of confounding environmental variation. This was investigated by comparing different maize lines grown within controlled environments. Rhizosphere bacterial communities were profiled by metabarcoding the universal bacterial 16S rRNA v3-v4 region. Initially, plants from the inbred B73 line and the traditional Ancho landrace were grown for 12 weeks and compared. The experiment was then repeated with an additional four Mexican landraces (Apachito, Tehua, Serrano, and Harinoso) that were grown alongside additional B73 and Ancho plants. In both experiments, there were significant compositional differences in the rhizosphere bacteria associated with different genotypes. Additionally, we found that genetic distance (phylogenetic) correlated with bacterial community similarity (i.e., more closely related lines had more similar rhizosphere bacteria). We therefore confirm that heritable variation in maize landraces is associated with differences in the rhizosphere bacterial communities. Further studies are required to identify the mechanisms that translate variation in the genome to predictable variation in the root microbiome, which could potentially be exploited to optimize the root microbiome for particular functions as part of crop improvement strategies.