Despite growing literature supporting the importance of home gardens (HG) as biodiversity hotspots, knowledge of patterns of their contribution to conservation of threatened species and crop wild relatives (CWR) across climate and culture in Africa is still limited. This investigation was conducted across three climatic zones to assess the floristic diversity of home gardens and the extent to which they contribute to conservation of threatened species and CWR. Overall, 240 home gardens were sampled and their floristic diversity assessed. The ecological importance of recorded species was determined per climatic zone using the importance value index (IVI). A cluster analysis was performed to group the species according to their IVI-values and a principal component analysis helped to identify the most important species. 285 species were inventoried throughout the study area. Home garden species’ diversity globally declined from the drier to the wetter zone but was highest in the transition zone. The average number of species found per HG was 10.1 and varied weakly across zones (9.07, Guineo-Congolean zone; 10.77, Sudano-Guinean zone; and 10.53, Sudanian zone). The most important home gardens species in the Sudanian, the Sudano-Guinean and the Guineo-Congolean zones were respectively: Abelmoschus esculentus (L.) Moench and Hibiscus asper Hook.f.; Solanum lycopersicum L. and Zea mays L.; Ipomoea aquatica Forssk. and Senna occidentalis (L.) Link. They were mainly vegetables and used as food and/or medicinal plant species. Twenty CWR and twelve threatened species were recorded and were also mainly used for food and medicinal purposes. Thorough research on socioeconomic factors supporting possession of HG and choice of managed species as well as indigenous management strategies of HG and dynamic of traditional knowledge related to HG may help to deeply assess home gardens’ effectiveness in biodiversity conservation.