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Colombia is part of the Andean centre of crop diversity—however, knowledge of plant genetic resources (PGR) (including farmers’ varieties, wild food and medicinal plants) in situ (on-farm and in the wild) is incomplete. PGR in Colombia are threatened by a range of factors, including a lack of appropriate policies to support their conservation and sustainable use, particularly by the indigenous rural communities that depend on local PGR (cultivated and wild), and play a vital role as custodians of this diversity. There is a critical need to increase the knowledge base for conservation planning and to inform the development of appropriate policies to avoid future loss of PGR diversity and the associated risks to the food, nutrition, health and livelihood security of these communities.