Bananas and plantains (Musa spp.) represent the fourth most important crop in the world. In 2017, an area of 5,637,508 hectares and a production of 153 million tons were reported. Fusarium wilt caused by the fungus Fusarium oxysporum f. sp. cubense (Foc), is considered one of the most destructive diseases of bananas and plantains worldwide. The pathogen Foc causes a typical wilt syndrome on infected plants, it has a saprophytic and parasitic phase in its life cycle. Fusarium wilt is a “polycyclic” disease. This pathogen shows a relatively diverse population genetic structure for a fungus apparently of asexual reproduction and is composed of different evolutionary lineages, which has 24 groups of vegetative compatibility (VCGs), two clades and nine clonal linage. Foc is a genetically diverse pathogen, although the available evidence so far indicates that it does not use the mechanisms of sexual reproduction, such as recombination, to increase its genetic diversity. Furthermore, the population of this fungus in Southeast Asia shows a high degree of variation, suggesting that Foc lineages evolved together with their hosts in Southeast Asia. Alternatively, it has been suggested that Foc has multiple independent evolutionary origins, both within and outside of the Musaceae origin center.