Understanding how species have responded to past climate changes might inform how current climate change may affect species. However, current perspectives on species' response to Quaternary cycles mainly stem from studies on mid and high latitudes and limited information is available at lower latitudes. In these systems a greater variation in individual species' responses to glacial cycles has been suggested, but we lack of clear case studies of such variations. Here, by means of ecological niche modelling, we characterized the niche differentiation of the five subspecies of the tortoise Testudo graeca in north Africa and described the range dynamics suffered by each of the subspecies since the Last Glacial Maxima. Molecular data was employed to infer past population dynamics. The five subspecies present a clear niche differentiation, particularly in relation to rainfall, covering a range from semiarid to humid species. The ecological differentiation among subspecies promotes very different, even opposite, post-glacial range dynamics. Since the Last Glacial Maxima, the ranges have either expanded (T. g. graeca), contracted (T. g. marokkensis), shifted northwards (T. g. soussensis) or remained stable (T. g. cyrenaica and T. g. nabeulensis). Molecular data supported the majority of these range dynamics. Our work exemplifies how, in a climate change scenario, phylogenetically very close taxa (i.e. at the subspecies level) might experience strikingly different biogeographical dynamics due to former niche differentiation. Our work supports an individualistic response to glacial cycles, which can be particularly strong in lower latitudes. In these areas precipitation changes during glacial periods may have strongly affected distribution ranges in idiosyncratic ways. We hypothesize that in those species limited by precipitation the response to glacial cycles (and climate changes) is more unpredictable than in those limited by temperature.