One of the keys to the success of the field of phylogeography is its flexibility and ability to integrate information from different fields, although arguably so far it has been unable to successfully incorporate demographic data in the inference process. We aim to contribute to fill this gap through a combination of modeling, field- and molecular-based approaches conducted at different geographic and temporal scales. This is illustrated through the analysis of two co-distributed amphibian species (Pleurodeles waltl and Pelobates cultripes), including 1) local (pond-based) studies producing data on local abundance (effective / census population size ratio) and fine-scale movement patterns; 2) regional studies describing landscape-level patterns of gene flow; and 3) range-wide studies including species distribution modeling (past and present environmental favourability) and analyses of multilocus datasets. Our approach highlights the need for an organismal, integrative and iterative phylogeography, continuously testing and producing new hypotheses on the origins of biodiversity. We also emphasize the practical (conservation) applications of this approach, for instance for the establishment of programs of long-term genetic monitoring.