Rhizobacteria that encourage plant growth are a crucial part of the intricate rhizosphere microbiome. It is frequently stated that the Pgpr community of various plant species is chosen by their rhizosphere, which favour the growth of some more than others. We evaluated the Pgpr community in the rhizosphere of significant plant species, including two cultivars and one landrace, in this greenhouse study utilizing the same agricultural soil. The landrace, cultivars, and rhizosphere all have different Pgpr community structures, although having comparable community structures. Exclusive Pgpr groups, which are implicated in plant resistance and stress tolerance, were found in the rhizosphere of the lima bean. Similar relative abundances of Bacillus and Paenibacillus, two groups engaged in promoting plant growth through the generation of antibiotics and biological N fixation, were found in the rhizosphere of both cultivars. Additionally, compared to landraces, cultivars showed a higher number of specialized microorganisms and more complicated community interactions. The results of this study add to our understanding of the Pgpr community in various plant species and support the importance of landraces and cultivars in determining the rhizobacteria community.