The full integration of time dimensions in GIS still represents a research challenge. A number of systems provide ways to visualise harmonised timestamped geographical data onto maps, with interpolated curves representing how these data have changed over time. However, these systems frequently mask the concerns linked to changes in territorial organisations and the harmonisation of data. In fact, the development of a territory should be considered in connection with its neighbourhood, governance and genealogy relationships. This article focuses on the difficulties linked with the ‘change of support problem’, which can arise when conducting spatio-temporal analysis of data. First, we present a data model handling the changing relationships between territories. Then, we illustrate how this model can be instantiated using examples that have taken place in Europe. We show how the model can address questions such as that of change blindness. Finally, we explain how hierarchical and genealogical relationships can be used inside an interactive cartographic tool for spatio-temporal analysis. It provides various views of the same phenomena at multiple scales, through an approach that takes into account the changes in territorial organisation.