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Setting conservation priorities with a geographic vision is essential in developing countries due to limited resources for conservation and the urgency of establishing new reserves. Priorities should reflect the risk ecosystems are facing and how represented they are in current national reserve networks (NRN). Conservation planning, research, and reserve design should focus on priority ecosystems. This study identified the priority ecosystems for the conservation of continental Ecuador’s biodiversity using a multi-criteria model developed in collaboration with Ecuador’s Ministry of the Environment. This model ranked ecosystems based on four conditions: representativeness in the current reserve network, human pressure, habitat loss, and species-level value based on bird species data. Results show that although Ecuador’s reserve network covers approximately 14% of the country, several ecosystems are poorly represented using a conservative 10% level benchmark, while others are not included at all. In general, highly diverse, humid environments are well represented while low-diversity, dry environments, are poorly represented. These low-diversity, low-representation ecosystems are also the most threatened. Conservation programs and new reserves design in continental Ecuador should concentrate on these ecosystems until the desired representativeness is attained. These results were formally presented to Ecuador’s Ministry of the Environment in 2000. This study shows that an ecosystem-risk-representativeness approach can be implemented efficiently at scales that take advantage of limited resources yet are effective for policy and planning. Current technologies can be used effectively to map major ecosystems, and to assess various forms of risk and representativeness in reasonable time for a country or a large region. [Copyright &y& Elsevier]