Bovine Tuberculosis caused by M. bovis represents an economic and animal health problem worldwide. In Mexico, the biogeography of M. bovis stemmed from studies using genotyping through several genetic markers obtained from SNPs, RFLPs, VNTRs, and Spoligotyping. More recent studies worldwide have used a combination of genotying and whole genome sequencing, in order to cover evolutive history, behavior, phylogeography of the strains. Not whole genome studies in M. bovis from Mexico have been made in detail since in SRA Genbank are deposited only the "reads" of the sequences of the M. bovis isolates. Therefore, in the present study, we focused to carried out the genome assembly of the reads from the SRA database. Phylogenomic analysis show that different isolates of M. bovis strains cluster in the same clade independent of the region, suggesting a close relationship between them. Collectively the data provide an update in the M. bovis phylogeography in Mexico.