Tuberculosis (TB) is one of the deadliest diseases from a single infectious agent, Mycobacterium tuberculosis (Mtb). Despite the multiple antibiotics available for TB treatment, due to overuse and misuse of these antibiotics, Mtb can acquire resistance against certain antibiotics and render them useless in treatment. These drug resistance cases increase significantly every year due to incorrect use of antimicrobial drugs and slow detection of resistance strains which result in more person-to-person transmission. These drug resistance strains have posed great threat in successful treatment. With acquired antibiotic resistance continuing to increase for Mtb, it is important to identify genes for strains that exist under specific adaptions such as antibiotic resistance, environmental condition, or lineage specific. Comparative microbial genomics strategy based on sequence similarity has become one of the popular methods to identify genetic content shared among all pathogenic isolates. Recently, whole genome sequencing has become faster, cheaper, and easier to access, increased the need for comparative microbial genomics analysis, or Pan-genome analysis, to compare these sequences data. A Pan-genome is the union of all the genes that exist in every member of a group of bacterial genome sequences. Mycobacterium Tuberculosis contains about four thousand coding genes, and each of these genes can have a variety of functions, whether they are responsible for virulence, cell envelope, regulatory, transportation, binding, or antigenic variation. The main purpose for this research is to identify possible correlation between genes present in clinical isolates and Mtb drug resistance with Pan-genome analysis. From this analysis, I hope to validate the mechanism of resistance for each antibiotic use to treat Mtb and possibly find an alternative mechanism of resistance in this study.