Background Blighia sapida is a woody perennial multipurpose fruit tree species native to the Guinean forests of West Africa. The fleshy arils of the ripened fruits are edible. Seeds and capsules of the fruits are used for soap-making and all parts of the tree have medicinal properties. Although so far overlooked by researchers in the region, the tree is highly valued by farmers and is an important component of traditional agroforestry systems in Benin. Fresh arils, dried arils and soap are traded in local and regional markets in Benin providing substantial revenues for farmers, especially women. Recently, ackee has emerged as high-priority species for domestication in Benin but information necessary to elaborate a clear domestication strategy is still very sketchy. This study addresses farmers' indigenous knowledge on uses, management and perception of variation of the species among different ethnic groups taking into account also gender differences. Methods 240 randomly selected persons (50% women) belonging to five different ethnic groups, 5 women active in the processing of ackee fruits and 6 traditional healers were surveyed with semi-structured interviews. Information collected refer mainly to the motivation of the respondents to conserve ackee trees in their land, the local uses, the perception of variation, the preference in fruits traits, the management practices to improve the production and regenerate ackee. Results People have different interests on using ackee, variable knowledge on uses and management practices, and have reported nine differentiation criteria mainly related to the fruits. Ackee phenotypes with preferred fruit traits are perceived by local people to be more abundant in managed in-situ and cultivated stands than in unmanaged wild stands, suggesting that traditional management has initiated a domestication process. As many as 22 diseases have been reported to be healed with ackee. In general, indigenous knowledge about ackee varies among ethnic and gender groups. Conclusions With the variation observed among ethnic groups and gender groups for indigenous knowledge and preference in fruits traits, a multiple breeding sampling strategy is recommended during germplasm collection and multiplication. This approach will promote sustainable use and conservation of ackee genetic resources.