This research focuses on the process of late transformation and final abandonment of Roman towns, on the Christianisation phenomenon and on the late antique evolution of settlement patterns in central Lusitania. The traditional explanations of sudden abandonments of Roman centres, due to "external" events, were swept away by a more scientific approach to archaeological evidence. The article presents data on the Late Antiquity phases of Ammaia and Ebora Iulia (today Évora). The results of a long period of archaeo-topographical research on the deserted Roman town of Ammaia (Marvão, Portugal), supported by international scientific collaborations, disclose new scenarios. On the basis of the survey data, integrated with the results of the recent ground-truthing excavations, it is possible to state that, from the beginning of the fourth century AD, the town seemed to be interested in a process of transformation and not of degradation. Évora was a bigger town and it was, from the fourth century AD, the seat of the diocese. In fact, it was one of the first towns of Lusitania and its bishop was present at the Council of Elvira (306/314 AD). Évora, unlike Ammaia, had continuity of occupation and therefore archaeological research has to deal with the problems usually connected with urban archaeology. The intention is to draw a short summary about the transformations that characterise the two towns in this period and, finally, identify common elements and differences.