Climate change and increasing habitat loss greatly impact species survival, requiring range shifts, phenotypic plasticity and/or evolutionary change for long term persistence, which may not readily occur unaided in threatened species. Therefore, defining conservation actions requires a detailed assessment of evolutionary factors. Existing genetic diversity needs to be thoroughly evaluated and spatially mapped to define conservation units (CUs) in an evolutionary context, and we address that here. We also propose a multidisciplinary approach to determine corridors and functional connectivity between CUs by including genetic diversity in the modelling while controlling for isolation-by-distance and phylogeographic history. We evaluate our approach on a near-threatened Iberian endemic rodent by analysing genotyping-by-sequencing (GBS) genomic data from 107 Cabrera voles (Microtus cabrerae), screening the entire species distribution to define categories of CUs and their connectivity: we defined six management units (MUs) which can be grouped into four evolutionarily significant units (ESUs) and three (putatively) adaptive units (AUs). We demonstrate that the three different categories of CU can be objectively defined using genomic data, and their characteristics and connectivity can inform conservation decision-making. In particular, we show that connectivity of the Cabrera vole is very limited in eastern Iberia, and that the pre-Pyrenean and part of the Betic geographic nuclei contribute the most to the species genetic diversity. We argue that a multidisciplinary framework for CU definition is essential, and that this framework needs a strong evolutionary basis.