The Dioscorea cayenensis - Dioscorea rotundata species complex is the most widely cultivated yam in West Africa. It has been described as deriving from wild types belonging to the species Dioscorea abyssinica and D. praehensilis from Enanthiophyllum section, through domestication by African farmers. Wild types were chosen on the basis of morphological criteria. In order to translate farmers' knowledge into standard descriptors and to assess whether domestication has a genetic base or not, 140 accessions of wild types D. abyssinica and D. praehensilis were collected in Benin. They were studied using IPGRI's yam descriptors, highlighting a continuum between the two species. A structuration of both species into domesticable and non-domesticable yams was observed. Based on 10 nuclear DNA simple sequence repeats (SSR), the molecular characterization leads to separation of D. abyssinica species into domesticable and non-domesticable groups. To establish phylogenetic relationships existing between wild and cultivated species, we investigated changes in chloroplast DNA simple sequence repeats (cpSSR) in a second collection compiled by 148 accessions selected to cover the genetic diversity existing in Benin. Dioscorea cayenensis and D. rotundata shared the same haplotype. The morphotype abyssinica appeared to be subdivided into 3 haplotypes from which one is shared with the D. cayenensis- D. rotundata species complex and with praehensilis morphotypes, suggesting that they might belong to the same species. Some taxonomic changes within the Enanthiophyllum section were suggested. Dioscorea minutiflora, D. smilacifolia, and D. burkilliana might also be suspected to belong to the same genetic group.