Crop wild relatives (CWR) encompass wild plant species or subspecies closely related to domesticated crops. This study presents the first comprehensive checklist and prioritized inventory of CWR for Sudan and South Sudan. Building on the regional CWR list for Northeast Africa, we identified 499 CWR taxa belonging to 44 families, with 90% of these being native species. The most prominently represented families were Poaceae (148), Fabaceace (72) and Convolvulaceae (43), while Panicum (32), Eragrostis (27), Ficus (24) and Pennisetum (20) were the most frequent genera. A prioritized inventory of 85 CWR taxa was developed based on three criteria: economic value, utilization potential and threat status. The prioritized CWR are predominately native (78%) and encompass 12 families dominated by Poaceae (38), followed by Solanaceae (9), Fabaceae (6) and Cucurbitaceae (6). Priority genera included 27, with Digitaria (17), Solanum (9) and Cucumis (5) emerging as key genera for conservation attention. This comprehensive national CWR inventory provides a crucial foundation for developing targeted conservation strategies in Sudan and South Sudan.