The rising need for crop diversification to mitigate the impacts of climate change on food security urges the exploration of crop wild relatives (CWR) as potential genetic resources for crop improvement. This study aimed at assessing the diversity of CWR of the Indian Ocean islands of Mauritius and Rodrigues and proposing cost-effective conservation measures for their sustainable use. A comprehensive list of the native species was collated from The Mauritius Herbarium and published literature. Each species was assessed for the economic value of its related crop, utilization potential for crop improvement, relative distribution, occurrence status and Red List conservation status, using a standard scoring method for prioritization. The occurrence data of the priority species were collected, verified, geo-referenced and mapped. A total of 43 crop-related species were identified for both islands and 21 species were prioritized for active conservation. The CWR diversity hotspots in Mauritius included Mondrain, followed by Florin and Le Pouce Mountain. Although a wide diversity of CWR has been recorded on both islands, most do not relate to major economic crops in use, therefore only a few species may be gene donors to economic crops at the regional and global level. For example, coffee, a major global beverage crop, has three wild relatives on Mauritius, which could potentially be of interest for future predictive characterization.