Harnessing this genetic diversity is crucial for enhancing crop improvement, ensuring sustainable agricultural practices, tackling climate challenges and meeting the demands of food security and better nutrition. This approach aligns with the goals of the European Green Deal, and the Biodiversity and Farm to Fork strategies, aiming to reduce pesticide use. Moreover, fruit trees’ long lifespan and a current production dominated by only few cultivars make them particularly vulnerable to the effects of global changes. Further research and conservation efforts are thus needed to unlock the full potential of fruit tree CWRs and secure our agricultural future.