Abstract Crop wild relatives are genetically related wild taxa of crops with unique resources for crop improvement through the transfer of novel and profitable genes. The in situ and ex situ conservation gap analyses for priority crop wild relatives from West Africa were evaluated using species distribution modelling, ecogeographic diversity, and complementary analyses. A total of 20, 125 unique occurrence records were used for the conservation gap analysis, however, 26 taxa had no occurrence data. 64 taxa (62.7%) occurred in protected areas, 56 taxa (55%) were conserved ex situ, while 76.7% (43) of the accessions are underrepresented with less than 50 accessions conserved ex situ. Areas of highest potential diversity were found in the Woroba and Montangnes districts in Cote d’Ivoire, Nzerekore, Faranah, Kindia, and Boke regions of Guinea, South-South, and North-East zones of Nigeria, and Kono and Koinadugu districts in Sierra Leone. Hotspots were found in Atlantique, Littoral, Mono, Kouffo, Atakora, Donga, and Colline provinces of Benin, Accra, and Volta regions of Ghana, North–Central Nigeria, and Lacs district of Cote d’Ivoire and Nzerekore region of Guinea. 29 reserve sites for active in situ conservation were identified, 11 occur in protected areas, while 18 are located outside protected areas. The establishment of the reserve sites will complement existing PAs and ensure long-term active in situ and ex situ conservation and sustainable utilization of priority crop wild relative to underpin food security and mitigate climate change in the region.