Cyclicity within the Late Miocene Tripoli and Calcare di Base Formations of Sicily was controlled by two processes: (a) partial evaporation of Palaeomediterranean waters but with periodic replenishment by Atlantic derived inflow on several occasions during the Late Tortonian and Messinian stages; (b) deformation of a regional foreland basin and associated satellite basins perched above south-verging sedimentary thrust sheets. These were intermittently set in motion by active plate collision onto the passive African Plate margin. Although it is not possible to discriminate fully the world eustatic signal under such a scenario, nevertheless, sufficient recolonization by marine faunas in these Sicilian basins occurred to permit modelling of onlap/offlap events for the Late Miocene intervals. Basin-wide correlation of these variably fossiliferous formations hangs on the recognition of a late Tortonian-early Messinian onlap event marked by coral reef development at the top of the Terravecchia Formation around the northern margins of the region. A further carbonate episode (Calcare di Base Formation) lies above a transgressive surface and directly overlies fluvial conglomerates at the top of the Terravecchia Formation around the northern margins of the basin. The Calcare di Base is partly diachronous with the top of the Tripoli Formation in the foreland basin but further north it oversteps the coral reefs on the southern margins of the Madonie Mountains. A variable number of internal Tripoli Formation cycles (confirmed on both faunal and sedimentological grounds) and Calcare di Base cycles (demonstrated only by sedimentation patterns), have been recognized. This minor cyclicity is considered to have resulted from periodic tectonic uplift and isolation of foreland basin and associated perched basins. This isolation controlled both influx of siliciclastic sediment and access by marine biota. Prolonged basin isolation during the deposition of the Tripoli Formation lead to rapidly declining diversity patterns in both benthonic and planktonic communities. Benthonic foraminifera disappeared early in many cycles with oligotypic planktonic foraminifera and radiolaria remaining longest. Under increasingly hostile conditions only diatoms remained. Each new cycle is marked at its base by a return to near normal conditions and a relatively diverse biota. Although faunas were stressed during the isolation events no clear evidence of salinity increase is seen. Rather we consider that a combination of oxygen depletion (especially on basin floors receiving prolific algal bioproduction) and toxin build-up (generally as the by product of algal metabolic processes) was the cause. The Calcare di Base cycles are more difficult to interpret on account of the virtual absence of biota. Here the cycles are clearly related to desiccation and salinity increase during times of restriction. The base of each cycle is marked by brine dilution and basin flooding, with some evidence of low diversity microfauna input in the early cycles. We envisage a Late Miocene palaeogeography with thrust-fold belts well established to the north of Sicily and a NE-SW oriented seaway developed ahead of them. To the south of this seaway lay an en-echelon belt of NE-SW oriented submarine ridges and localised basins which effected a sill, or at times a barrier, between the seaway and the Tripoli basins. A broad diatom-dominated perched basin complex extended along the southern margin of the thrust-related ridges and was intimately linked to a broad foreland basin, also diatomitic, lying immediately to the south. The foreland basin was separated from a further open sea area in southern Sicily by a second NE-SW oriented sill now hidden by later overthrusting. It is suggested that similar tectonic scenarios were responsible for isolating diatomaceous basin elsewhere in the Mediterranean during late Miocene times.