M. bovis had largely been considered as possessing one or very few copies of the insertion sequence 6110 (IS6110), which rendered IS6110-based genotyping methods unsuitable for strain characterisation. Nevertheless, using an IS6110-PCR as a first line detection method for bovine tuberculosis (bTB) in cattle, we observed variable detection results depending on the genotype of the infective strain, suggesting that IS copy numbers could be variable among them. Our work therefore aimed at studying by in silico analysis the copy numbers and location of the IS6110 on the genomes of a panel of 87 strains that reflect the French M. bovis population's genetic diversity to assess if this element could play any role in genome plasticity and in the bacterium phenotype.