On the basis of a combined larger benthic foraminifera, nannofossil and strontium isotope dating programme we confidently re-assign muddy carbonate deposits from the Lower Kinabatangan River Area of Borneo to the Oligocene rather than the Early Miocene. High-diversity, coral-rich (>. 50 species) deposits are here tightly constrained to predominately at, or just after, the Early to Late Oligocene boundary (Larger benthic foraminifera zone - Te1, Nannofossil zone - NP24, Sr isotope ages - 28.8-27.6. Ma). This new dating potentially pushes back the start of the Indo-West Pacific Centre of Marine Diversity, at least for corals, about 5. million years earlier than previous data indicated. Our new data supports maintaining separation of the muddy carbonates (previously defined as the Lower Kinabatangan Limestones: Haile & Wong, 1965) from nearby crystalline limestones of the Gomantong Limestone Formation dated here as Early Miocene (Larger benthic foraminifera zone - Te5/earliest Tf1, Sr isotope age - 21.0. Ma). This apparently punctuated development of shallow marine carbonates is seen at several locations in northern Borneo; an area underlain by oceanic crust and long dominated by very deep marine sedimentation (Hutchison, 2005). The opportunistic formation of clastic-influenced coastal and isolated biohermal carbonates is both an important palaeontological data point and a geological marker of changing basin settings. The new data on the first shallow marine deposits in a long established deep marine location, and evidence for unconformities, has important implications for the regional tectonic model, in an area of hydrocarbon exploration.