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In the last decade, robust sequencing technologies have revolutionized the genomic science. As a result, comparative genomics is now recognized as a new discipline. Comparative microbial genomics exploits both similarities and differences in the genomes, proteome, trascriptome, and regulatory regions of different organisms to infer the evolutionary relations, along with conserved and unique characteristics of species. These analyses have resulted in some surprising biological discoveries in the recent past. This study presents comparative genomic analysis of multiple pathogenic and non-pathogenic bacteria from related species, to dissect the genomic information and to get insights into evolutionary relationships, conserved information and mechanisms of pathogenicity. Starting from genus Corynebacterium, 11 representative species are analysed and compared, resulting in 741 conserved Gene Families (GFs) in all of them, and significant intra-species proteome similarities (98-99%) were observed. Subsequently, the pan- (7059 GFs) and core genome (552 GFs) of genus Campylobacter is estimated. A detailed comparative pathogenomic study of Campylobacter fetus subspecies resulted in identification of common and novel regions associated with pathogenicity; and species specific virulence factors and vaccine candidates have been characterized. Furthermore, comparative genomics and pathogenomics analysis of the genus Helicobacter (46 genomes) is accomplished. 38 Helicobacter pylori were found to share 1,185 core gene families representing ~77% of the average genome size. The core essential genes families (EGFs) are ascertained, and explored for potential therapeutics against H. pylori. In conclusion, we propose that, these observed genomic variations, species specific features and core virulence factors will enhance understanding of the lifestyle of the organisms, and will contribute to the development of antibiotics, drugs and vaccines.