Societal impact statementGlobal yam production is centred on West Africa, but there are significant knowledge gaps about farm‐level diversity across much of the region, and especially in Guinea. Although yam production is increasing in Guinea, in the longer term, varietal diversity and the sustainability of agri‐systems are at risk. Documentation of local crop diversity is essential as a baseline to understand trajectories of past and future varietal loss. This study utilises interdisciplinary approaches, which are needed to help understand the ways historic crop diversity is created and maintained within indigenous agricultural and food heritage systems, as well as the reasons for its loss over time.Summary Yams are important staple foods in many tropical and sub‐Saharan countries. The ‘yam belt’ extends from Guinea to western central Africa. However, yam cultivation is comparatively little researched or documented in Guinea, and the country is commonly not included within descriptions of key yam growing areas in Africa. Our study utilises ethnobotanic methods and plant specimen collections to fill these gaps in West African yam research. Interviews with over 70 farmers from six villages across the Kankan region of Guinea provide information on yam cultivation and diversity, and changes in living memory over the past 40 years. We present the analyses of ethnobotanical data from Haute‐Guinée on yam cuisine, and commercialisation, and on changes to the range of varieties grown over time. The annual cycle of indigenous yam agri‐systems remains a key part of rural life, food systems and economy. However, interviews revealed dramatic temporal changes over the last 40 years. Although yam production has increased, a narrow range of commercial cultivars is currently displacing the historically‐rooted local diversity. The expansion of yam cultivation is regarded locally as having relied on a shift to more unsustainable and extensive land use, and with herbicides and chemical fertilisers replacing intensive organic soil management. This has implications for research and development in sub‐Saharan agriculture for yams and other important native West African crops in the future.