A key issue in bacterial phylogeny is to understand how different bacterial species are related to each other and their branching order from a common ancestor. Currently most phylogenetic trees are based on 16S rRNA or other genes/proteins. These trees are not always able to resolve key phylogenetic questions with a high degree of certainty. However in recent years the discovery and analyses of conserved indels (CSIs) in many universally distributed proteins have aided in this quest. The genetic events leading to them are postulated to have occurred at important evolutionary branch points and their species distribution patterns provide valuable information regarding the branching order and interrelationships among different bacterial phyla.