Banana bacterial wilt caused by Xanthomonas campestris pv. musacearum has caused significant decline in livelihoods dependant on the banana/musa enterprise in the great lakes region of Eastern Africa. First line control methods using cultural packages are not sustainable for long term application and yet resistant material is yet to be availed to the producers. The pathogen is also largely unknown and thus the need to understand host pathogen interaction at the molecular level. Recently, affordable genome sequencing has eased the application of genomic, post-genomic, and functional genomic approaches to problems of direct relevance to parasitic diseases in plants, humans and animals. Comparative genomic analysis of xanthomonas species pathogenic on musa was conducted as a means of unraffling the virulence factors associated with these strains. It refers to discovering how have Xanthomonas spp. are adapted for host- and tissue-specific pathogenesis, understanding bacterial plant pathogenesis and host- driven pathogen adaptation and potential to develop practical applications for crop protection through better disease control and prevention.