The class Gammaproteobacteria forms one of the largest groups of bacteria. It is currently distinguished from other bacteria solely by 16s rRNA-based phylogenetic trees. No molecular characteristics unique to the class or its different subgroups are known. A detailed CSI-based study was conducted to better understand the phylogeny of this class. Firstly, a phylogenetic tree based on concatenated sequences of a number of universally-distributed proteins was created. The branching order of the different orders of the class Gammaproteobacteria (from most recent to the earliest diverging) was: Enterobacteriales >Pasteurellales >Vibrionales, Aeromonadales >Alteromonadales >Oceanospirillales, Pseudomonadales >Chromatiales, Legionellales, Methylococcales, Xanthomonadales, Cardiobacteriales, Thiotrichales. Additionally, 4 CSIs were discovered that were unique to most species of the class Gammaproteobacteria. A 2 aa deletion in AICAR transformylase was uniquely shared by all gammaproteobacteria except for Francisella tularensis. A 4 aa deletion in RNA polymerase b-subunit and a 1 aa deletion in ribosomal protein L16  were found uniquely in various species belonging to the orders Enterobacteriales, Pasteurellales, Vibrionales, Aeromonadales and Alteromonadales, but were not found in other gammaproteobacteria. Lastly, a 2 aa deletion in leucyl-tRNA synthetase was commonly present in the above orders of the class Gammaproteobacteria and in some members of the order Oceanospirillales. Another CSI-based study has also identified 4 CSIs that are exclusive to the order Xanthomonadales. Taken together, these two facts show that Xanthomonadales is a monophyletic group that is ancestral to other Gammaproteobacteria, which further shows that Xanthomonadales is an independent subdivision, and constitutes one of the deepest-branching lineages within the Gammaproteobacteria clade.