This paper presents the results of a study on nannofossil assemblages in the uppermost Messinian and basal Zanclean sediments recovered from Ocean Drilling Program (ODP) Holes 969B (south of Crete) and 967A (north of the Eratosthenes Seamount) located in the Eastern Mediterranean Sea. Focus of the research is on (1) the micropaleontological signature of the basically nonmarine facies of the uppermost Messinian interval; (2) the correlation of the Messinian/Zanclean boundary outside the Mediterranean by means of nannofossil biostratigraphy; and (3) the mechanism of sapropel formation in the earliest Pliocene. The main results are summarized as follows:1. The Messinian sediments are characterized by assemblages dominated by diagenetic resistant and long-ranging Neogene species, absence of typical upper Tortonian-Messinian species, high abundance of reworked taxa of Cenozoic and Cretaceous age, and high abundance of gypsum crystals and dolomite. All evidence listed above point to the absence of a primary marine signature in the nannofossil assemblages of the sediments. A noticeable exception, constituted by anomalous abundance of Sphenolithus spp., which suggests a possible (marginal) marine signature, is documented.2. The recovery of some specimens of Triquetrorhabdulus rugosus and of Ceratolithus acutus overlapping each other in the basal Zanclean suggests that, contrary to what has been reported by most authors, the last appearance datum (LAD) of T. rugosus and the first appearance datum (FAD) of C. acutus do not exactly coincide. This was already reported from the Ceara Rise (ODP Leg 154), where the FAD of C. acutus was found immediately below the cyclostratigraphically correlated position of the Messinian/Zanclean boundary. These closely spaced bioevents can be considered as a valuable tool, in addition to magnetostratigraphy and astrocyclostratigraphy, for the recognition and worldwide traceability of the Messinian/Zanclean boundary.3. Based on a model by Molfino and McIntyre, fluctuation in abundance of Florisphaera profunda, a peculiar nannoplankton species living in the lower part of the photic zone, is interpreted to represent nutrient availability within different levels of the photic zone. Thus, positive peaks of F. profunda were connected by the author to the presence of a deep chlorophyll maximum (DCM) at times of sapropel formation, a concept previously introduced by Rohling and Gieskes for the mid-Pleistocene to Holocene time interval.Abundance peaks of Florisphaera profunda are recorded in all five sapropel layers recovered in the basal Zanclean of ODP Hole 969B. Therefore, the DCM model may be tentatively applied also to the earliest Pliocene and probably to the whole sapropel sequence of the Mediterranean area, since the late Miocene.The recovery of abundance peaks of Discoaster pentaradiatus in most sapropels (together with the decreased abundance of Coccolithus pelagicus in some of them), suggests that these sapropels probably correlate with the marls (and not the limestones) of the rhy...