Ecuador has been recognized as one of the 17 megadiverse countries in the world. It present a great variety of native crops preserved thanks to traditional agricultural practices of indigenous communities. The GEF-funded project “Integrate the use and conservation of agro-biodiversity in public policies” sought to overcome the many threats affecting biodiversity while reducing rural poverty. The project contributed to enhance food security and the livelihoods of family farmers by supporting the sustainable use of local crops and developing short marketing circuits. The project also supported the integration of agrobiodiversity in the National Strategy for Biodiversity and in the Development and Land Management Plans at provincial level. It was instrumental to the formulation of the Agrobiodiversity and Seeds Law, the development of a database of 546 native seeds and to the establishment of Bio-knowledge and Agricultural Development Centers. Future projects should continue supporting national and local governments in regulating and implementing the Agrobiodiversity and Seeds Law, in establishing the National Agrarian Authority and creating a niche in the national and international market for native crops.