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A new methodology combining the concepts of endemicity and threat in order to provide an objective and highly accurate selection of protected areas is defined. This is a new method to recognize areas of endemism which combines the results yielded by NDM program, based on the optimality criterion, and those obtained using MARXAN software, designed to ensure the representation of species in the management of biodiversity. The method has been tested using the endemic and threatened vascular flora of the South of the Iberian Peninsula (Andalusia). Eleven areas of endemism have been identified in this territory; Sierra Nevada, Sierra Bermeja and Sierra Tejeda y Almijara stand out primarily. Although most of the areas dealt with in our study are already efficiently protected, the intermountain depression known as the Hoya de Baza, an arid area, and Sierra de Gador are exceptions. This new methodology provided a useful tool in the fine-tuning of the selection of areas of endemism. A more precise and flexible selection of scale-dependent endemicity areas was accomplished in this manner. The combination of both criteria (endemicity and threat) not only provides a reliable representation of areas of endemism, but also optimum efficiency in terms of endemicity and presence threatened of species. This approach offers a more objective and flexible strategy which can be implemented on different scales. A lot of alternatives can be generated, so the same conservation objective can be achieved by different combinations of solutions. This is a great advantage for the prioritization of territories meriting conservation. (C) 2014 Elsevier GmbH. All rights reserved.