Introduction and objectives. Paratuberculosis or Johne's disease is a chronic intestinal disease caused by Mycobacterium avium ssp. paratuberculosis (Map), primarily affecting ruminants and present worldwide. Despite the implementation of control programs in most developed countries, and the consequent financial efforts required, the prevalence rate of paratuberculosis remains very high, at around 50% in European herds and 8% in U.S herds. This worrying situation is due to a lack of knowledge about the biology of this pathogen and its transmission dynamics. Map's genomic studies, initiated in 2016, have recently multiplied thanks to the development of 3rd generation sequencing. Here we present a review of the contribution of Map genomic studies to our understanding of this pathogen and the epidemiology of Johne's disease. Materials and methods The articles collected for this synthesis encompass more than 820 genomes available in the NCBI SRA, GenBank, and ENA databases and 15 complete genomes. Map strains were distributed over 5 continents and have been isolated from a variety of hosts but mainly ruminants. We selected studies for which epidemiological data were available. Results, discussion and conclusion Analysis of the pangenome shows that Map is a clonal species with a core genome of 98%. The advent of next-generation sequencing has not only made it possible to establish relationships down to the strain level, but has also revealed genome-wide differences between strains, making it possible to establish Map's population structure by country and between countries. Phylogenetic analyses combined with data on animals, including their movements, provide a better understanding of Map's transmission dynamics. Map genomics has also revealed the notion of mixed infection in animals. Taken together, these data further our knowledge of this pathogen and offer new prospects for improving the prevention and control of Johne's disease.