Crop-related wild plant species are a rich source of genetic diversity and are potentially useful in plant breeding for the development of varieties with novel traits. However, many crop wild relatives are poorly represented in gene banks, while their continued survival in situ is by no means ensured. Here we introduced a methodology to inventory relevant taxa and to assess their threat levels for continued survival in situ, including the expected effects of climate change, and applied it to crop wild relatives in The Netherlands. A total number of 214 taxa of wild relatives of economically important agricultural and horticultural crops were identified, of which 53 are included in the Dutch red list of plant species. The group of 53 red list species was studied in more detail to prioritize species for conservation. Based on recent distribution data, the number of Dutch populations consisting of at least 50 individuals varied strongly among the red list species. The majority of these ‘large’ populations were found to be located in protected areas. Furthermore, niche modelling was used to study the expected effects of climate change on the future distribution of the red list species. These analyses predicted a reduced distribution area for the majority of species, although also positive effects of climate change were observed for several species. Similar patterns of change were observed when only protected areas were considered. Results of the study were used to prioritize the conservation of crop wild relatives in The Netherlands.