<p>Currently centered on molecular data, bacterial and archaeal relationships are often based on their relative branching in 16S rRNA based phylogenetic trees. The availability of numerous bacterial genome sequences over the past two decades has provided new information for insights previously inaccessible to the field of taxonomy. Through utilization of comparative genomics, numerous molecular markers in the form of insertions and deletions within conserved regions of proteins, also known as Conserved Signature Indels or CSIs, have been discovered for various prokaryotic taxa. Using these techniques, we have analyzed relationships among the bacterial phyla of Thermotogae and Synergistetes and the conglomeration of bacterial organisms known as the PVC super-phylum. Through identification of large numbers of CSIs we have described the phyla Thermotogae and Synergistetes, and their sub-groups, in molecular terms for the first time. The identified molecular markers support a reconstruction of the current taxonomic divisions of these phyla. Similarly, previously only observed to group in phylogenetic trees, we have identified molecular markers for the PVC clade of bacterial phyla which are indicative of their shared ancestry. Further, in response to recent suggestions of extensive lateral gene transfer masking evolutionary relationships, an argument in favour of Darwinian mode of evolution for prokaryotic organisms is made using the identified molecular markers identified here along with markers previously identified in similar studies. Due to their taxonomic specificity, the markers that we have discovered provide useful tools for biochemical tests aiming for an understanding of the unique characteristics of the bacterial groups to which they are specific.</p> / Master of Science (MSc)