AbstractThe region with the highest marine biodiversity on our planet is known as the Coral Triangle or Indo-Australian Archipelago (IAA)1,2. Its enormous biodiversity has long attracted the interest of biologists; however, the detailed evolutionary history of the IAA biodiversity hotspot remains poorly understood3. Here we present a high-resolution reconstruction of the Cenozoic diversity history of the IAA by inferring speciation–extinction dynamics using a comprehensive fossil dataset. We found that the IAA has exhibited a unidirectional diversification trend since about 25 million years ago, following a roughly logistic increase until a diversity plateau beginning about 2.6 million years ago. The growth of diversity was primarily controlled by diversity dependency and habitat size, and also facilitated by the alleviation of thermal stress after 13.9 million years ago. Distinct net diversification peaks were recorded at about 25, 20, 16, 12 and 5 million years ago, which were probably related to major tectonic events in addition to climate transitions. Key biogeographic processes had far-reaching effects on the IAA diversity as shown by the long-term waning of the Tethyan descendants versus the waxing of cosmopolitan and IAA taxa. Finally, it seems that the absence of major extinctions and the Cenozoic cooling have been essential in making the IAA the richest marine biodiversity hotspot on Earth.