the last decade. Methods exist for deciding how to use scarce information and avoid omission and commission errors. The effect of these errors on reserve efficiency does not arise only from the accuracy of data representing conservation features, as usually considered. There are also several underlying assumptions associated with the type of data used that might affect accuracy of conservation decision-making and compromise achievement of conservation objectives. 2. Here the effects of two management scenarios on selection of priority areas for conservation are explored. The spatial distribution of 10 native freshwater fish species in an Iberian basin under present-day and reference conditions were modelled and priority areas for both scenarios using the same spatial and cost constraints were identified. 3. Priority areas identified under the present-day scenario reflected the up-to-date spatial distribution of species and avoided the selection of highly perturbed and costly areas. The isolated spatial distribution of native populations imposed by the current perturbation status limited the spatial connectivity between priority areas under the present-day scenario. Most importantly for the achievement of conservation objectives, priority areas selected under both scenarios did not overlap. 4. Given that the reference scenario was based on potential presence of native species the actual representation of species would be overestimated if consideration were not given to restoring reference conditions (high commission errors). Based on results obtained it is recommended that planners give more consideration to the current perturbation status when identifying priority areas for conservation.