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Endemic taxa are those restricted to a specific area, and could be defined as the exclusive biodiversity of a region. An area of endemism contains taxa found nowhere else and could be catalogued as irreplaceable and of high priority for conservation. proposed the parsimony analysis of endemicity (PAE) as a tool to detect areas of endemism. PAE, a method of historical biogeography, is analogous to cladistic methods used in phylogenetics analysis, and unites areas (taxa in cladistics) based on their shared species (characters in cladistics) according to the most parsimonious solution. In this paper we determined with PAE, prioritary areas for conservation on the basis of concentrations of endemic species in the arid region of Antofagasta, northern Chile, and compared the results with their representation in the current Chilean National Parks and Reserves System. We found two areas suggested as priorities, one located in the north Andean zone of the region, and another at the coast. The area with the higher biodiversity and concentration of endemics was that located at the coast. However, coastal ecosystems are currently under-represented in the Chilean National Parks and Reserves System. The establishment of a new protected area in the coastal zone of the region of Antofagasta is currently under consideration, coinciding with the area suggested with PAE as priority. This new area would not only allow conserving species with evident problems of conservation, but also preserving an area where higher levels of endemism exist.