Sediments deposited after the peak of the Messinian Salinity Crisis (MSC) in the Apennine foredeep of Italy embody a topic debated on both chronostratigraphic and palaeoenvironmental grounds. We performed micropalaeontological (calcareous nannofossil and dinoflagellate cyst) analyses on four stratigraphic sections (Monticino, Civitella del Tronto, Fonte dei Pulcini, Fonte la Casa) and reused those previously published from Maccarone. All sections belong to the p-ev2 Fm. that includes the Colombacci deposits, usually considered emblematic of the Lago Mare in the area. Marine microfossils recorded in previous studies have often been neglected or considered reworked and hence discarded. We propose the occurrence of at least four marine inflows between 5.36 and 5.33 Ma, the first of which is reflected in the Apennine foredeep by marine dinoflagellates that are then replaced by Paratethyan (brackish) ones. Paratethyan species occupied favourable environments during intervals separating marine inflows while the marine species survived elsewhere. From this perspective, the Apennine foredeep was an isolated perched basin during most of the peak of the MSC (5.60–5.36 Ma), and was progressively and repeatedly invaded by marine waters overflowing a palaeo-sill before the beginning of the Zanclean (5.33 Ma) which itself reflects a continuing eustatic rise. The Gargano Peninsula and, offshore, the present-day Pelagosa sill may be regarded as the remnants of this Messinian sill. This interpretation provides new possibilities for ecostratigraphically correlating the sections with Lago Mare biofacies, the deposition of which unquestionably started prior to the deposition of Colombacci sediments and continued into the earliest Zanclean. The results of this study show that the Lago Mare facies cannot be restricted to a single brackish palaeoenvironment but included competing marine and brackish waters controlled by geographic and chronological factors. Deposits overlying the unconformity separating the regional p-ev1 and p-ev2 formations are considered to represent the first marine incursion into the Apennine foredeep. These results allow us to refine the palaeogeographic reconstruction of the Apennine foredeep during the peak of the MSC. Although this basin was deep, its history during the peak of the MSC did not parallel that of the central Mediterranean basins.