Fonio, known to be the smallest and oldest form of millet grown in sub-Saharan Africa, has remained relatively poor of research despite its nutritional, sociocultural, agroecological, therapeutic and economic potentials. Based on systematic literature review, this critical study showed that fonio genetic breeding progress is at a low level. Genetic resources are threatened by erosion, particularly extra-early cultivars of Digitaria exilis, and mainly D. iburua species have practically disappeared in some cultivation countries including Benin. Varietal environment is characterized by lack of improved varieties and seeds, so that cultivars are ecotypes derived from natural selection often with low yields. Seeds, very tiny, are generally heterogenous, in polyvarietal mixtures because of unimproved systems and management by farmers. These ecotypes are susceptible to stem lodging and seed shattering. An exhaustive list of fonio genetic resources from West and Central Africa into catalog remains to be documented. There is a need for regional and international networking of fonio researchers with institutional support for harmonizing germplasm characterization methods, will facilitate descriptors development for all countries. It is necessary to consider in this work wild relative species that have potential genes of resistance/tolerance to biotic and abiotic stress. Starting from autogamy and apomixis revealed on fonio, homogenization program using pureline and mass selection of cultivars could enable rapid release of homogeneous and higher yielding materials to farmers and processors. Development of early and yielded varieties, with upright stem and coarse grains, resistant to lodging, shattering, and facilitating mechanical harvesting would enhance effective production revival.