The present-day global maximum for marine biodiversity has been located in Southeast Asia since at least the earliest Miocene. The history of biota in the region has been inferred from the present-day biogeography and phylogeny of extant organisms, but these analyses do not provide adequate tests of the various hypotheses proposed for the origins of the diversity hotspot. The papers in this special issue present the results of an interdisciplinary research project designed to reconstruct the history of shallow marine biota and habitats within the hotspot and help understand the ecological context responsible for the maintenance of the diverse regional biota. A series of remarkably complete and fresh exposures were studied from the Kutai Basin (East Kalimantan, Indonesia) that included thick lower to upper Miocene sections of deltaic and marine sediments including abundant and extremely well preserved fossils. New stratigraphic and environmental frameworks allowed comparison of biota from habitats ranging from shelf-edge reefs to nearshore shallow seagrass meadows and coral carpets. Diversity was overall high throughout the interval, especially when compared to diversity in similar modern turbid mixed carbonate-siliciclastic settings. This points to the previously unrecognized importance of these mesophotic habitats for the development of the diverse reef-associated communities in the modern-day hotspot.