The Pyrenean population of Spanish wild goat (Capra pyrenaica pyrenaica) is nearly extinct. To find the most appropriate source of individuals for supplementing the Pyrenean population, we identified Evolutionary Significant Units (ESUs) among populations of the Capra pyrenaica species. We have examined sequence variability of portions of the mitochondrial DNA (mtDNA) control region and cytochrome b (cyt b) gene. Samples were from seven populations of Spanish wild goat distributed over the species' geographic range. The level of divergence between the Pyrenean and other Spanish haplotypes is almost as high as the divergence between the Alpine (C. ibex ibex) and the Spanish wild goats. In addition, the Pyrenean goat is morphologically distinct from other Spanish wild goats. Therefore the Pyrenean population should be considered as an ESU. For the reinforcement, we suggest either using individuals from the most polymorphic Spanish population, or mixing individuals from diverse Spanish origins, since all the other Spanish populations are equally genetically distant from the Pyrenean population.