Within-species genetic diversity is crucial for the persistence and integrity of populations and ecosystems. Conservation actions require an understanding of factors influencing genetic diversity, especially in the context of global change. Both population size and connectivity are factors greatly influencing genetic diversity; the relative importance of these factors can, however, change through time. Hence, quantifying the degree to which population size or genetic connectivity are shaping genetic diversity, and at which ecological time scale (past or present), is challenging, yet essential for the development of efficient conservation strategies. In this study, we estimated the genetic diversity of 42 colonies of Rhinolophus hipposideros, a long-lived mammal vulnerable to global change, sampling locations spanning its continental northern range. Here, we present an integrative approach that disentangles and quantifies the contribution of different connectivity measures in addition to contemporary colony size and historic bottlenecks in shaping genetic diversity. In our study, the best model explained 64% of the variation in genetic diversity. It included historic bottlenecks, contemporary colony size, connectivity and a negative interaction between the latter two. Contemporary connectivity explained most genetic diversity when considering a 65 km radius around the focal colonies, emphasizing the large geographic scale at which the positive impact of connectivity on genetic diversity is most profound and hence, the minimum scale at which conservation should be planned. Our results highlight that the relative importance of the two main factors shaping genetic diversity varies through time, emphasizing the relevance of disentangling them to ensure appropriate conservation strategies.