Crop wild relatives (CWR) have proven to be very valuable in agricultural breeding programs but remain a relatively under-utilized and under-protected resource. CWR have provided resistance to pests and diseases, abiotic stress tolerance, quality improvements and yield increases with the annual contribution of these traits to agriculture estimated at USD 115 billion globally and are considered to possess many valuable traits that have not yet been explored. The use of the genetic diversity found in CWR for breeding provides much-needed resilience to modern agricultural systems and has great potential to help sustainably increase agricultural production to feed a growing world population in the face of climate change and other stresses. A number of CWR taxa are at risk, however, necessitating coordinated local, national, regional and global efforts to preserve the genetic diversity of these plants through complementary in situ and ex situ conservation efforts. We discuss the absence of adequate institutional frameworks to incentivize CWR conservation services and propose payment for ecosystem services (PES) as an under-explored mechanism for financing these efforts. Such mechanisms could serve as a potentially powerful tool for enhancing the long-term protection of CWR.