Phylogenetic trees are the traditional way to represent evolutionary relationships. However, they fail to adequately represent species evolution even with the sequencing of whole genomes. To address this issue we utilized a novel modeling technique, the phylogenetic rings and applied our methods to the relationships among the proteobacteria, which is the most speciose proteolytic phylum known in science, containing free living, pathogenic, photosynthetic, sulfur metabolizing, and symbiotic species. We develop new rooted ring analyses and studied proteobacterial evolution using protein family data and outgroup rooting procedures. We discover and map the origins of significant gene flows in the rooted proteobacterial rings, and recognized that the evolution of “Alpha-”,”Beta-”, and “Gamma”-proteobacteria is represented by unique set of rings. Our analyses utilize gene presences and absences to determine complex gene flows. Thus, unlike trees which only show branching arrangements, our graphs depict the complex flow of genes producing phenotypes. Through our analyses we are able to identify the gene flows that led to photosynthesis in Alpha-, Beta-, and Gamma-proteobacteria from the common ancestor of the Actinobacteria and Firmicutes. From our study of the rooted rings of proteobacteria we find consistency with the observed genotypic and phenotypic relationships observed among the various proteobacterial classes. Ring phylogenies can explain the evolution of both genotypes and phenotypes of biological processes in robust and complex groups such as proteobacteria.