There is an extensive diversity of crops and their wild relatives in Mexico, which are distributed throughout the country. Crop wild relatives (CWR) play a special role for present and future food security strategies: they represent a potential source of variation for the domesticated species, contributing to the genetic improvement of these crops. However, the effects of climate change, among other threats, are reducing significantly this biodiversity. The purpose of this study was to analyse the diversity of wild relatives of the most important crops in Mexico as a basis for the development and implementation of a national conservation strategy for these genetic resources. The methods involved the identification of priorities and creation of a national CWR inventory, in situ and ex situ gap analyses at taxon and ecogeographic levels, the evaluation of the impacts of climate change, threat assessment and predictive characterisation. Applying these methods, 310 CWR taxa were identified as priorities and recommendations for immediate in situ and ex situ conservation actions were made to ensure their representativeness under current and future climatic conditions. All these components contribute to the systematic active long-term conservation of priority CWR diversity in the country and enhance their sustainable utilisation thus helping mitigate the threats to Mexican agrobiodiversity and global food security.