In bacteria, transcription generated positive and negative supercoils are removed by DNA gyrase and topoisomerase I acting ahead and behind the transcribing RNA polymerase (RNAP) to overcome the topological barriers. We have investigated in vivo recruitment and interaction of both the topoisomerases with mycobacterial genome. We have mapped the genome-wide footprints of topoisomeraseI and DNA gyrase along with RNAP in the deadly pathogen, Mycobacterium tuberculosis(Mtb), taking advantage of minimal topoisomerase representation in the organism. We show that in vivo distribution of topoisomerases is guided by active transcription and both the enzymes co-occupy active transcription units (TUs). The recruitment was higher at the genomic loci with higher transcriptional activity and/or at regions under high torsional stress compared to silent genomic loci. We establish their interaction with the regions of genome having propensity to accumulate negative and positive supercoiled domains, validating their role in managing the twin supercoiled domains. Next, we have probed genome wide action by trapping enzyme- DNA complexes - either by using chemical inhibitors or poisonous mutants. Comparison of these genome wide action sites with binding sites determined by Chip Seq provide insights into topoisomerase I function in transcription elongation and chromosome segregation.