Bacteria are critical to the health of eukaryotes and the ecosystems in which they persist. Some symbiotic interactions are mutualistic in which both microbe and host benefit from the partnership. Other interactions are parasitic, and the microbe typically benefits at a cost to the host. Rhodococcus is a genus of bacteria in which members are frequently associated with plants. We sought to model the evolution of phytopathogenic lineages and mechanisms of virulence of Rhodococcus. Findings demonstrated that the acquisition of a plasmid carrying three loci implicated in virulence can transition Rhodococcus bacteria from being potential mutualistic bacteria to pathogenic bacteria. Findings also showed that the virulence fasR, carried by the plasmid is necessary but not sufficient for phytopathogenicity of Rhodococcus. Last, we report results from molecular genetic approaches, that are important for resolving conflict in the annotations of the coding sequence of fasR. The work described in this thesis highlights how the acquisition of a small number of genes can have a profound effect on symbiosis of plant-associated bacteria and provides a foundation for testing how FasR, a predicted transcriptional regulator co-opts for pathogenicity the genes encoded on the chromosomes of Rhodococcus.