Many basins are filled under the influence of tectonics and variable climatically driven processes. Unravelling the relative contributions of these is generally easier in fossiliferous sequences if faunal diversity patterns are considered in conjunction with lithofacies analysis. This approach has been successfully applied to Late Miocene strata of Sicily, where progressive restriction and desiccation within the Sicilian Caltanissetta region occurred under a semi-arid climate during the Messinian Stage. This restriction was partly due to Antarctic cooling which produced Palaeo-Mediterranean sea-level oscillations during the Early Messinian, as a prelude to closure of the Atlantic connections. In addition, regions within this Afro-European plate collision zone were also subjected to syndepositional tectonic deformation associated with progressive perched basin development above foreland (south) verging thrust sheets. The relative impacts of climatic (eustatic) versus tectonic control on sedimentation patterns within these perched basins has been debated at length. However, progress towards resolving this problem by a combined approach involving lithofacies analysis, and faunal phase analysis provides clues for separating the effects of the controlling factors. Faunal phase analysis identifies general faunal associations with minimal emphasis on species diversity. The resulting ‘phase’ plots for Early Messinian strata appear to be transgression skewed when controlled by eustatic cyclicity, and regression skewed when driven by regional tectonics associated with perched basin tectonics.