The Mycobacterium genus includes diverse pathogenic and non-pathogenic species. Cattle and wildlife are also affected by Mycobacterium avium subspecies paratuberculosis , which is responsible for paratuberculosis or Johne's disease; this disease is widespread globally and represents an important source of animal suffering and economic loss. This chapter presents examples of pathogenic Mycobacterium infections of animals. Whole-genome sequencing has facilitated construction of the most reliable phylogenetic trees of Mycobacterium strains to date. The pathogenesis of mycobacterial disease largely depends on the immunoregulatory cell envelope. This highly structured and complex entity is a virulence factor per se that comprises unique lipids and glycolipids. Sigma factors, some of which are involved in virulence and pathogenesis, form part of a tightly regulated network. In mycobacteria, iron acquisition is mediated by small, soluble iron chelators called siderophores.