Abstract Methodology of cyclostratigraphic analysis applied to benthic foraminifera is verified utilizing a faunal and geochemical dataset,from the Middle Miocene Ras il-Pellegrin composite section (Malta Island, central Mediterranean). Benthic data were elaborated by Q-mode varimax principal factor analysis. In this paper, spectral analysis is carried out only on two factors, which have a clear paleoecological significance: Factor 1 (loaded by Cibicidoides ungerianus and Siphonina reticulata), indicative of oxic bottom waters, and Factor 2 (loaded by Bulimina elongata group), indicative of oxygen-stressed conditions. Results of these analyses show that Factor 1 and Factor 2 curves are,respectively, in and out of phase with maxima of the eccentricity (100 d 400 ky). We utilize the 3D paleocenographic model of Bellanca et al. (2002) as reference for the Middle Miocene Mediterranean circulation and focus our attention on the Mediterranean Intermediate water, characterized by hydrographic and hydrodynamic features similar to those presently recorded in the Levantine Intermediate Water (LIW). Consequently, we suppose that Middle Miocene Mediterranean Intermediate Water, here defined as proto-MIW, played a role similar to that of present Mediterranean Intermediate Water (MIW). Following this hypothesis, Factor 1, which is indicative of oxic bottom waters, is interpreted as a tracer of high production of proto-MIW, during periods of high eccentricity and, probably, precession minima, characterized by coldest winter seasons. These results point out a direct link between selected benthic species, long-term astronomical forcing, and deep-water response and provide a useful tool for astronomical calibration of geologic time and for paleoceanographic reconstructions.