Cyprus is one of the few areas of the Mediterranean where lower and upper Miocene coral-reefs occur in close proximity and is thus well suited to investigate how environmental and geological changes affected the reefs and their associated shallow-marine facies. The prevailing environmental conditions of the lower Miocene Terra Member and of the upper Miocene Koronia Member are reconstructed here, using detailed microfacies comparisons of the skeletal, foraminiferal and calcareous algal assemblages. The lower Miocene reefs are characterised by a higher biodiversity of coralline algae, large benthic foraminifera and corals, and mainly developed in slightly deeper water (20–40 m, lower euphotic zone) than the upper Miocene reefs (< 15 m; upper euphotic zone). The reduced late Miocene biodiversity was probably caused by changes in the Mediterranean marine environment (e.g. increased seasonality), possibly in response to global cooling, increased latitudinal gradients and progressive isolation of the basin. The observed shift of the reef environment towards the upper euphotic zone could be explained as a response to late Miocene physical oceanographic setting, notably temperature changes, which could have made the upper euphotic zone more favourable for certain hermatypic corals. Similarities between the Miocene carbonate facies of Cyprus and the Eratosthenes Seamount directly to the south, and elsewhere in the Mediterranean region (e.g., Corsica; Italy; Spain), suggest that the environmental changes inferred for the Miocene of Cyprus operated on a Mediterranean or even wider scale.