This article presents the results of a coring operation which brought to light new evidence for the evolution of the coastal plain of Aulis (Boeotia, Central Greece) in the Holocene. Thanks to Homer, Aulis is best known as the gathering point of the Achaean fleet before it sailed to Troy and a sanctuary of the goddess Artemis. Ancient sources and archaeological evidence suggest the presence of an ancient marine bay, potentially used as a harbor. In the course of investigation, we drilled two cores, to a maximum depth of 4.20 m in the marshy lowlands and performed mollusc and micro-paleontological identifications, laser grain size analyses, and magnetic susceptibility measurements in order to reveal the facies evolution of the area. We obtained a chronostratigraphy sequence through a series of seven AMS 14C radiocarbon dates. Our study shows that the area was affected by a shallow marine incursion from the first half of the 6th millennium BC and gradually turned into a succession of shallow marine/lagoon environments from ca. 5000 cal. BC to the 2nd Century AD, and into a confined lagoon environment during the Roman and Byzantine periods.