Brazil is one of the most biodiversity rich countries in the world, including a wealth of agricultural biodiversity in both wild and cultivated forms. This is particularly noticeable in southern Brazil, home to a wide array of underutilized food species whose genetic diversity is maintained mostly by farmers through on-farm management practices. Farmers’ contribution in safeguarding and keeping alive traditional knowledge (TK) essential for recognizing, cultivating, valorising and consuming these resources is critical to their conservation. Part of this diversity, a rich basket of native fruits and landraces of vegetables and grains, is also maintained through ex situ collections managed by Brazilian Agricultural Research Corporation (Embrapa) and its partners. This article discusses the integrated efforts for in situ/on-farm and ex situ conservation and use of agricultural biodiversity in southern Brazil. This diversity represents an important cultural heritage, since its use, cultivation and associated knowledge result from the dynamic history of the Brazilian population, including colonisation and immigration by several different ethnicities. Many of these species are sources of genes that convey tolerance to biotic and abiotic stresses, as a result of the combined action of natural selection and artificial selection by farmers in agricultural systems with low inputs and diverse environmental conditions. Due to their importance for food security, use in breeding programs, high nutritional value, and potential for income generation, Embrapa has taken responsibility for the ex situ conservation of these species. The genebanks that safeguard against the loss of these resources do also play an important role in the restoration of this germplasm to farming communities.