Disturbance events play an important role in ecosystem services management and species biodiversity. In this sense, species biodiversity may constitute a large proportion of the total ecosystem value, mainly in natural protected areas. The present research proposes a methodology for the economic valuation of flagship species; the value of charismatic species was estimated using two complementary approaches based on recovery programs and contingent valuation method (CVM). While recovery programs approach is related to government expenditure, CVM is associated with survey results according to the society's willingness to pay. There are significant differences between both approaches as flagship species are highly valued by the society. In this sense, a difference of 43.75% on the species value can be found depending on the scenario of CVM (all respondents or only affirmative respondents). Our research was done on the integration of economic tools and wildfire severity of two burned areas in order to evaluate the effects caused in their habitat and, as a consequence, in the food chain. The results obtained from both the studied areas emphasized the importance of wildfire impacts on flagship species (209,619.08-445,495.88 € from Doñana wildfire and 634.68-5792.98 € from Segura wildfire) which are often omitted in valuation reports. The use of Geographic Information Systems helps to identify flagship species impacts per unit area (74.89-159.17 €/ha from Doñana wildfire and 0.76-6.98 €/ha from Segura wildfire) and to prioritize restoration activities on the most susceptible areas. This methodology could be extrapolated to any territory and spatial resolution based on the revision of the questionnaires regarding flagship species. The availability of cartography of flagship species´ susceptibility could play a critical role in budget optimization and the decision-making process on restoration planning.