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In previous centuries, wolves were extirpated across much of their range worldwide, but they started to recover in Europe since the end of last century. A general pattern of this recovery is the expansion of the range occupied by local populations. The Iberian wolf population, shared by Portugal and Spain, reached its lowest extent and abundance around the middle of the twentieth century. Unlike other populations in Europe, its range recovery and pack counts seem to have stalled since the first Spanish country-wide census of 1986–1988. The population shows low effective population size and remains isolated from other European wolves. This is unexpected given the protection offered by European legislation, i.e., the Habitats Directive, and the apparent availability of habitat outside its present range. We compiled records of wolves killed legally in Spain, reviewed the legislative and management framework for the Iberian wolf population, and discussed potential implications of a policy of lethal management for the ecology, genetics and conservation status of wolves in the Iberian Peninsula. Wolves are strictly protected in Portugal. Meanwhile, they are subject to culling and hunting in Spain. No wolf was legally removed by culling or hunting during the study period in Portugal, whereas 623 wolves were legally killed in Spain between 2008 and 2013. Twenty-nine of those wolves were killed in areas under strict protection according to European legislation. Despite the transboundary nature of this wolf population, we are not aware of coordinated conservation plans. Management is further fragmented at the sub-national level in Spain, both due to the authority of Spanish autonomous regions over their wildlife, and because wolves were listed in multiple annexes of the Habitats Directive. Fragmentation of management was apparent in the uneven adherence to the obligations of the Habitats Directive among Spanish regions. A similar situation is found for other large predator populations in Europe. We suggest that lethal management as carried out in Spain is a hindrance to transit and settlement of wolves, both within and beyond the Iberian wolf population. Reducing the pressure of lethal management appears a feasible policy change to improve the conservation status of the population and foster transboundary connectivity.