Plant growth-promoting rhizobacteria (PGPR) are free-living soil bacteria (the rhizosphere bacteria) that can either directly or indirectly facilitate the rooting and growth of plants. They have been introduced in modern agriculture as a new practice to enhance crops’ sustainable growth and productivity. Rhizomicrobiome plays key roles in nutrient acquisition and assimilation, improving soil texture, secreting, and modulating extracellular molecules such as hormones, secondary metabolites, antibiotics, and various signal compounds, all leading to enhancement of plant growth. The genetic diversity of PGPR shows multiple differences due to the influence of many factors on the genetic composition in the long term. The most important factors are the types of cultivated plants, the type of soil and its geological structure, the geographical location, and the farmers’ agricultural activities. Species of culturable bacteria such as Bacillus spp., Pseudomonas spp., and Acinetobacter spp., among others, have been used as PGPR. While traditional identification is not enough for exact identification, new approaches such as DNA fingerprinting, phylogenetic analysis, gene expression, and metagenomic sequencing are currently used to study the genetic diversity of PGPR and reveal its genetic pathways. This chapter will discuss the genetic diversity of PGPR, including promising species and functions, factors, and genetic approaches.