Biodiversity is currently experiencing exceptional loss due to the activities of humans, negatively impacting the ecosystem services on which humanity relies. Additionally, human-induced climate change is already negatively impacting agriculture worldwide – a trend that will only worsen – leading to reduced yields for some crops and regions. Crop wild relatives (CWR) the wild cousins of domesticated crops contain a wide breadth of genetic diversity not found in cultivated crops, which can be used for breeding new climate tolerant varieties. However, CWR is under-conserved in the wild, thus jeopardizing this resource. Funds for CWR conservation activities are often limited; to conserve efficiently therefore, conservation strategies could prioritize in situ actions in areas of existing biodiversity conservation or protection, so long as CWR diversity overlaps with other components of biodiversity (i.e., other taxa). This analysis examines whether CWR could benefit from being conserved in biodiversity hotspots. Global CWR hotspots were defined from statistically significant spatial clustering of areas of high CWR richness. Biodiversity hotspots had significant overlap with CWR hotspots with the highest coincidence in the Mediterranean basin (91%) and the California Floristic Province (91%). Overall, the Mediterranean basin, Irano-Anatolian, Caucasus and Tropical Andes hotspots showed the greatest promise for in situ conservation of CWR, and hence greater efficiency of conservation investments.