In this study we report the reannotation of the genome of seven Mycobacterial species and subspecies. We have used bioinformatics tools for annotation and reevaluated each of the Protein-Coding Sequences (CDS) previously annotated and presented the combined results of recent database searches. We have also used comparative genomic tools to focus on comparative analysis as an effective strategy. Pair wise comparison between the various Mycobacterium strains was performed so as to predict the relationships between them. Among the wide variety of mycobacterium strains present, we selected seven and showed how their genome is interrelated by studying synteny with the genomes of various strains studied. The genome wide SNP analysis in the seven genomes of Mycobacterium sp. was also done in this study and the base by base changes in the genome of these seven subspecies were identified. The gene based SNPs were further classified into the marker SNPs (SNPs which are unique amongst all the seven studied species). Out of a total of 2073 SNPs, 966 were identified as marker SNPS. This study may be used for further analysis of host pathogen interactions at the pathway and product level. The present investigation will also be useful for study of evolutionary relationship.