Due to the global trends in biodiversity loss, there is an increasing need in conservation biology for the development of methodologies to aid in the fast development of conservation management guidelines. This work focuses on combining methodologies from conservation and landscape genetics with predictive modelling and connectivity, to provide relevant insights on the ecological and molecular characteristics of bat cryptic species, while presenting significant outputs for conservation management. Using the Iberian Peninsula as a case study, this research firstly aimed at determining the distributions, as well as ecological and biogeographical affinities, of recently discovered bat cryptic species. These outputs revealed possible unsurveyed areas of species occurrence as well as the ecological relationships between species' niches and the contact zones within each cryptic complex. With a particular focus on the poorly-known cryptic lineage Plecotus auritus begognae, a population evolution study was also developed to clarify the evolutionary history and relationships between the Iberian Plecotus lineages. These results revealed a clear separation of all lineages within this genus, except between Plecotus auritus auritus and Plecotus auritus begognae, which were only differentiated by mitochondrial DNA and microsatellites, therefore suggesting a recent separation and supporting the subspecies status. Successful field campaigns were then conducted in the previously determined subspecies' area of occurrence, with the aim of filling the sampling gaps. Subsequently, a multi-disciplinary approach was developed, integrating landscape genetics' analyses with species distribution modelling and connectivity methodologies, to study the environmental drivers affecting the population structure and connectivity patterns of P. a. begognae. This subspecies showed no clear population structure within Iberia, with gene flow occurring throughout its range. The outputs of this study, however, not only demonstrated that this gene flow is dependent on the presence of forested and mountainous areas, but also identified the subspecies' distribution patches which are potentially at-risk of isolation. The large extents of mature forests in the North of the Iberian Peninsula seem to be preventing the fragmentation within this subspecies and, as such, conservation efforts directed to forest preservation in these areas are recommended. Finally, with the aim of evaluating the potential impacts of climate change in P. a. begognae's populations, landscape genetics was integrated with climatic modelling. The results obtained showed a considerable contraction of P. a. begognae's suitable area of occurrence for 2050 and even more severe for 2070. Most of the subspecies' distribution range will become unsuitable, forcing populations to shift their ranges into projected suitable and stable areas, mostly located in north-western Iberia. The most likely pathways for range shift and dispersal, and the climatic predictors most related to them were also determined. Predictions also revealed possible refuge areas, as some regions located within the western distribution of the subspecies seem to remain stable throughout the decades in climate change scenarios. Overall, the integration of different disciplines proved successful in providing relevant ecological and molecular information for P. a. begognae, as well as presenting spatially explicit outputs essential to prioritize conservation measures.