Proteobacteria is one of the largest and phenotypically most diverse divisions within the domain bacteria. Due to the economic importance, this phylum demands an urgent need for a clear and scientifically sound classification system to streamline their characterization. The goal of our study was to carefully reevaluate the current system of classification and suggest changes wherein necessary. Phylogenetic trees of 84 Proteobacteria were constructed using single gene-based phylogeny involving 16S rRNA genes and protein sequences of 85 conserved genes, whole genome-based phylogenetic tree using CVtree3.0, amino acid Identity matrix tree, and concatenated tree with aforementioned conserved genes. The results of our study confirm the polyphyletic relationship between Desulfurella acetivorans, a Deltaproteobacteria with Epsilonproteobacteria. The group Syntrophobacterales was found to be polyphyletic with respect to Desulfarculus baarsii and the group Thiotrichales was found to be splitting in different phylogenetic trees. Placement of phylogenetic groups belonging to Rhodocyclales, Oceonospirilalles, and Chromatiales is controversial and requires further study and revisions. Based on our analysis, we strongly support reclassification of Magnetococcales as a separate class Etaproteobacteria. From our results, we conclude that concatenated trees of conserved proteins are a more accurate method for phylogenetic analysis, as compared to other methods used.