The detailed micropaleontologic study of the sedimentary series overlying the youngest ophiolitic basalts of the Troodos massif (Cyprus), confirms the late Campanian age of the top of the oldest terrigenous cover (Kannaviou Formation) topping these ophiolites themselves assigned to Cenomanian-Turonian. It also demonstrates for the first time the strong diachronism of the Lefkara Formation chalky limestones, unconformably overlying either the Kannaviou Fm. sandstones and clays, or the oceanic basalts. This diachronism over short distances and the on-lap of the Lefkara Fm. are revealed by varying stratigraphic gaps within the Paleocene-Miocene interval and are indicated by new age datings of the transgressive basal part of the Lefkara Fm. along six principal sections: late Thanetian (Zone P5) at the Pano Lefkara typelocality; early Ypresian (Sub-zone P6a) at Agia Anna; earliest Bartonian (Zone P13) at Kannaviou and Analiontas; early-middle Lutetian (Zones P10 to P11) at Kofinou; Langhian (Zone N8) at Choulou. Maastrichtian deposits are missing and Maastrichtian Globotruncanidae/Heterohelicidae only observed as individual reworked specimens within well-dated Tertiary levels. Finally, we discuss the influence of the Tertiary extensional brittle tectonics on this diachronism, the on-lap processes and the differential subsidences occurring after the late Cretaceous/? early-middle Paleocene folding (Laramian compression).