The fall armyworm (FAW), Spodoptera frugiperda, a major agricultural insect pest in the Western Hemisphere, currently also poses a significant threat to many cereal crops in Africa. FAW consists of two morphocryptic strains, the corn- and the rice strains, which were thought to display typical genetic, physiological and behavioural features. However, this is not absolutely true, rendering direct identification and distribution of the strains impossible in field. Thus, to investigate 1) the composition and diversity of FAW strains, 2) their distribution at various spatial scales, and 3) the host plants they use, in invaded countries we used the COI barcode fragment, a marker capable of accurately distinguishing the two strains. A total of 125 specimens mainly sampled on maize in Niger and Senegal and to a lesser extent in Guinea, Mali, Togo, Burkina Faso and Cape Verde were analyzed. Sixteen haplotypes were identified among which two occurred very frequently. Phylogenetic analysis delineated two lineages, the rice and corn strains, but no typical geographical and host-plant patterns were found. The FAW-strain haplotypes derived from West African specimens were genetically comparable with those sampled elsewhere in Africa, the Americas and Asia. Considering all sites and plants sampled, the corn strain slightly predominated but on maize, the two strains were statistically comparable. Their distribution is largely sympatric at region, field and even maize plant scales. These findings are compared to populations recorded elsewhere and are discussed in the framework of biological invasions, and the management and ecology of the species.