After more than two decades of implementation of the Habitats Directive (Directive 92/43/EEC), some fundamental aspects of the directive are still unclear, and subject to interpretive uncertainty, which limit its correct implementation. For example, obligations for Member States in situations where a protected population has almost, or has just, gone extinct are unclear. The isolated and protected population of wolves (Canis lupus) in the Sierra Morena region in Spain – the only wolf population in the southern half of the Iberian Peninsula – has been steadily declining to the point where it is doubtful whether any wolves are left. Using this illustrative example, we provide clarifications on the obligations by Member States in situations where populations are on the verge of extinction. Our analysis shows that Articles 6 and 12 of the Habitats Directive require Member States to restore populations that are quasi extinct. From a legal perspective, even the complete extinction of the species would not exonerate Member States from its obligations regarding the species in the Natura 2000 sites concerned. In this line, we argue that the Spanish authorities should not wait with recolonization, reinforcement and/or reintroduction actions until the complete absence of wolves in the Sierra Morena is conclusively proven. Two scenarios appear to meet legal requirements: i) active reinforcement/reintroduction, or ii) an active and effective policy towards a rapid natural recolonization of Sierra Morena by northern wolves. However, based on the observed wolf trends in Spain and Portugal during the past five decades, a reconnection between northern and Sierra Morena wolves seems unlikely in the foreseeable future even if actively promoted. Considering the urgency of actions required to avoid that this population will be the first wolf population to become extinct in Europe in modern times, in order to comply with European obligations, the adopting and carrying out a reintroduction/reinforcement scheme to restore the Sierra Morena wolf population is required. Such a scheme needs to be accompanied by a comprehensive enforcement plan to assure that reintroduced wolves will thrive.