The census of natural populations provides relevant information for both conservation purposes and environmental monitoring. In the present work, natural populations of the killifish Aphanius fasciatus (Teleostei: Cyprinodontidae) were censused in the Italian territory. The historical distribution of the species was reconstructed with the aid of bibliographic material and museal samples, in order to evaluate the extent of changes in its distribution. Three periods (pre-1990s, 1990s, post-1990s) and five habitat types (lagoons/coastal ponds, saltworks, canals, river mouths, inland water bodies) were considered. Overall, we recorded the presence of A. fasciatus in 82 localities, the majority of which are lagoons/ponds. The species showed a widespread decline and sometimes local population extinction, due to habitat degradation and competition with the introduced poeciliid Gambusia holbrooki. With a few exceptions, A. fasciatus is currently extinct in inland waters, being mainly present in coastal brackish-water habitats. The occurrence of stable populations along the central Tyrrhenian, northern Adriatic, Sardinian and Apulian coastal biotopes is confirmed. The populations of Sicilian inland waters, considered extinct, showed recovery capabilities. In northern Tuscany, where the species was also considered extinct, there are also recent records. From a temporal perspective, the present work shows that A. fasciatus experienced population reductions throughout its range in the 1990s, when the species appeared locally extinct, or strongly rarefied, in several localities. Since then, the species recovered in the majority of the native range. However, careful monitoring is needed in order to control the effects of habitat alterations and competition with G. holbrooki on natural populations of A. fasciatus. Given the importance of brackish-water habitats as both biodiversity hotspots and buffer areas against rainfalls and floods, A. fasciatus may be raised to the status of "umbrella species" with regard to these habitats.