The class Gammaproteobacteria and its different main orders are currently classified solely on the basis of their branching in phylogenetic trees. In most cases, no molecular, biochemical or physiological characteristics are known for their demarcation. The availability of genomic sequence data has enabled the discovery of two types of molecular characteristics in the forms of Conserved Signature Indels (CSIs) and Conserved Signature Proteins (CSPs) that provide novel means for identification and demarcation of prokaryotes. In the following work, numerous CSIs and CSPs have been identified for different orders within the class Gammaproteobacteria, with particular focus on Pasteurellales, Xanthomonadales and “Enterobacteriales”. The order Pasteurellales contains a single family, Pasteurellaceae, harbouring many important human and animal pathogens. We have discovered a large number of novel CSIs that are specific for either all Pasteurellales or several distinct clades within this order of bacteria. Based upon these CSIs, we have been able to demarcate the “sensu stricto” members of the genera Actinobacillus, Haemophilus, and Pasteurella that are presently polyphyletic. Similarly, we have identified numerous CSIs for the phytopathogens-containing order Xanthomonadales and have used them in conjunction with phylogenetic analyses for the taxonomic reorganization of the members of this order. The Xanthomonadales species that branched monophyletically and shared CSIs were grouped into one of two families within the order Xanthomonadales while the other species were transferred to a new order. This work also reports many CSIs and CSPs for the phytopathogenic genera Dickeya, Pectobacterium and Brenneria from the order “Enterobacteriales” and this work also discusses the usefulness of CSIs and CSPs for understanding prokaryotic systematics and taxonomy. Additionally, based upon the species distribution of CSIs, we have also examined the impact of LGT on prokaryotic phylogeny/systematics. The extensive work on CSIs that we have reviewed supports the notion that the genetic changes responsible for them have been inherited predominantly in a vertical manner following Darwinian mode of evolution. The molecular markers discovered in this work, because of their taxa specificities, provide valuable means for genetic and biochemical studies that should lead to discovery of novel biochemical and physiological characteristics of the studied groups of bacteria and they also provide new tools for their diagnostics and as potential drug targets for these bacteria. / Thesis / Doctor of Philosophy (PhD)