The role of farmers and their production constraints and preferences are important for sweetpotato breeding and adoption of cultivars and agronomic production packages. The objective of this study was to assess farmers’ perception, production constraints, preferences, and breeding priorities of sweetpotato in selected agro-ecologies of Rwanda. A total of 495 farmers were surveyed in 2013 in eight representative districts: Bugesera and Kayonza in the Eastern Province, Gakenke and Rulindo in the Northern Province, and Gisagara, Huye, and Muhanga in the Southern Province. Data were collected through a participatory rural appraisal (PRA) methodology using a semistructured questionnaire and focus group discussions. Pairwise comparison of 16 food crops allocated sweetpotato as one of the five important food crops for food security and income generation. Drought stress, unavailability of improved cultivars and planting material, and pest and disease damage were perceived to be the five main constraints limiting sweetpotato production, contributing to 17.3%, 15.0%, 12.9%, 11.7%, and 11.5%, respectively. The most important sweetpotato cultivar traits had high yield, early maturity, drought tolerance, disease and pest tolerance, and good culinary taste at 22.5%, 18.5%, 15.4%, 12.7%, and 10.1%, respectively. The characteristics of good storage roots identified by farmers included high dry matter content, good culinary taste, good shape, root size, and sweetness representing 27.4%, 18.8%, 16.1%, 11.6%, and 9.4%, respectively. Each agro-ecological zone has its own specific sweetpotato production constraints and farmers’ preferences, necessitating targeted breeding of different sweetpotato cultivars for each agro-ecological zone for enhanced productivity and successful adoption of cultivars.