During the last years, the exponential growth of human population has entailed a dramatic effect on the global biodiversity. Large carnivores have been one of the greatly affected in this biodiversity crisis. Despite apex predators, such as wolves, have apparently increased their distribution range in Europe during the 21st-century, local declines and lack of gene flow between fragmented populations might be hindering the recovery of these carnivores. Specifically, in the Iberian Peninsula, the Iberian wolf (Canis lupus signatus) has remained isolated from the rest of the European wolf populations since 19st-century. During decades, the distribution of the Iberian wolf has been divided in two populations separated by intensive urban and agricultural areas, the Northwestern population and the Southern population, a smaller population located in Sierra Morena. The decline of the Southern population may have made it increasingly vulnerable in an extinction vortex, in which a combination of low population size and negative environmental and genetic factors spiral the population toward extinction. The main objective of my thesis is to understand the evolutionary history of Iberian wolves through the integration of ecological and genetic/omic approaches. In my thesis, I will address biological questions related with genetic diversity, fragmentation and patterns of connectivity in recent and past wolf populations in the Iberian Peninsula by analyzing modern, historic and ancient DNA.