The rhizosphere microbiome is pivotal for plant growth and health, contributing to nutrient acquisition and stress tolerance. Microbiome assembly is driven in part by the plant genotype, but little is known about the impact of plant domestication on microbiome assembly of economically important food crops. Here, we investigated rhizobacterial community composition in modern and wild accessions of common bean (Phaseolus vulgaris) grown in agricultural soil from the highlands of Colombia, one of the centers of common bean diversification. DArT-based genotyping and phenotyping of local common bean accessions showed substantial genetic and root architectural differences between wild and modern bean accessions. Wild accessions showed a higher specific root length and root density than the landrace and modern accessions. Rhizobacterial community analyses combined with modelling showed that species abundance is explained by niche-based distributions, with 13.5% of the variability in community composition determined by the bean genotype. Along a bean genotypic trajectory going from the most ancestral to the most modern (based on inbreeding coefficient and homozygosity), we observed a gradual decrease in the relative abundance of Bacteroidetes, mainly Chitinophagaceae and Cytophagaceae, and an increase in relative abundance of Actinobacteria and Proteobacteria, in particular Nocardioidaceae, and Rhizobiaceae. Collectively, these results indicate that domestication of common bean affected rhizobacterial community assembly.