Phylogeography and ecological niche modelling are two key approaches advancing biogeography. A special issue of Folia Zoologica (64: 2015) considers these advances in eight articles, including two reviews—on Next Generation Sequencing (NGS) and Ecological Niche Modelling (ENM)—and six research articles, plus two book reviews. The reviews on NGS and ENM stand out as the main interests of the issue. The six research articles provide different biogeographical case studies in which phylogeography and ENM are used together, representing a timely comparison of the current most common practices and the advances highlighted by the reviews.