The natural vanilla essence is obtained principally from the fruits of the species Vanilla planifolia, a member of the Vanilla aromatic clade, and native to the neo-tropics. Colombia is an important center of diversity for the genus with 22 Vanilla species reported, of which 18 belong to the aromatic clade. Colombian native Vanilla species comprise important genetic resources for the vanilla crop. Although there is no tradition of cultivation of vanilla in the country, these species have potential for establishment in sustainable agroforestry systems. Nonetheless, Vanilla, like many orchid species, is subject to both intrinsic and extrinsic conservation threats. This article outlines an integrated strategy for conservation, incorporating in situ, ex situ and circa situm measures to ensure the conservation of Vanilla species in Colombia, and to promote their sustainable use in community-based cultivation programs. This proposed strategy is also relevant for conservation managers in other countries with native Vanilla species.