Plant genetic resources characterization is essential for their conservation and their use in both breeding strategies and adaptation to global change. This is all the more important for species often neglected by research such as fonio. Fonio refers to two indigenous small millets grown in West Africa, white and black fonio (Digitaria exilis and Digitaria iburua, respectively). This research was carried out to develop a simple and reliable method to identify the two cultivated species of fonio in the context of genebank collection. A morphometric analysis was performed on seeds of 98 accessions of D. exilis and 20 accessions of D. iburua. Morphometric characters measured were seed dimensions, shape and colour. We showed that the major delimiting criterion was the seed width and that the seeds of black fonio were wider than those of white fonio. The proposed method, based on seed morphometrics, could be applied systematically in conservation routine to guarantee the accuracy of the passport data in fonio collections, as well as to identify fonio remains for archaeological studies.