Study of the extinct and extant biota of the Coral Triangle region has not yet provided answers to questions about mechanisms controlling the origins and maintenance of this marine biodiversity hotspot. We present an updated stratigraphy and revise the taxonomic determinations for important historical collections from Indonesia that have been the basis of our knowledge of the history of the region for the past 150 years. Revision of the stratigraphy increases the resolution of ages assigned to most of the collections, and shifts a significant number of coral occurrences from the Pliocene to the late Miocene revealing a new Pliocene sampling gap. The previously recognized Paleogene sampling gap remains open. Analysis of taxonomic turnover with unrevised and revised data show similar overall patterns, with an early Miocene increase in richness followed by a plateau of relatively high richness. Overall, the observed pattern of taxonomic turnover is highly correlated with sample size, suggesting that uneven sampling may be a more important control on the data pattern than processes of speciation and extinction. Highly correlated turnover patterns of zooxanthellate and azooxanthellate taxa are also consistent with this interpretation. The paucity of Paleogene data in the historical collections means that the prevailing paradigm of Neogene origins of high richness in the modern Coral Triangle remains a tautological default hypothesis. New collections are required to adequately estimate rates of taxonomic turnover in the region, and to reconstruct the structure and functioning of ancient ecosystems during the origins of the Coral Triangle biodiversity hotspot.