The genus Dioscorea (Dioscoreaceae) contains several economically important species for human consumption, medical and pharmaceutical uses. The phylogeny of this genus is not yet resolved. As a result, the relationships between cultivated yams and their wild relatives are not well understood and this negatively impacts the understanding of cultivated yams' evolution. Here, we reconstructed the phylogenetic relationships of the main African cultivated species with all West African species in order to better circumscribe the Crop Wild Relatives of African yams. Complete chloroplast genomes of 57 individuals representing all know 17 Dioscorea species from West Africa were reconstructed. Phylogenetic analyses recovered using neighbourjoining, maximum parsimony or maximum likelihood approaches were highly congruent. We recovered six monophyletic groups corresponding to seven botanical sections. All species were clearly distinct except within the Enantiophyllum section, where it was not possible to separate the two main cultivated species (D. rotundata and D. cayenensis) from their closest wild relatives (D. abyssinica, D. praehensilis and D. sagittifolia). Dioscorea baya was well differentiated but closely related to the cultivated clade. We therefore suggest its integration within the yam Crop Wild Relative complex.