In an attempt to discriminate between tectonically induced sea-level changes and glacio-eustacy, the Ekklissia and Arakthos sections (Epirus, NW Greece) are examined, applying (dinocyst) palynology, sedimentology and magnetostratigraphy. The sections, located in the Pindos Foreland Basin, both comprise the transition from pelagic limestones to hemipelagic silty clays and turbidite sandstones, reflecting the onset of flysch sedimentation as a result of the Pindos thrust activity. Despite an overall tectonic overprint, relative changes of sea level can be reconstructed, using (i) continental/marine palynomorph ratios, (ii) relative abundance of inshore and offshore dinoflagellate cysts, and (iii) taxa indicative of relatively cold and warm sea-surface temperature, that can be calibrated against the Global Polarity Time Scale (GPTS). Increased fluxes of marginal marine and continental palynomorphs coincide with colder periods on a 'third-order' scale, which thus appear to be related to glacio-eustatic trends in sea-level. The larger scale is attributed to the increasing effect of tectonics and acts on a 'second-order scale'.