Hotspots of tropical marine biodiversity are areas that harbour disproportionately large numbers of species compared to surrounding regions. The richness and location of these hotspots have changed throughout the Cenozoic. Here, we review the global dynamics of Cenozoic tropical marine biodiversity hotspots, including the four major hotspots of the Indo-Australian Archipelago (IAA), western Tethys (present Mediterranean), Arabian Sea and Caribbean Sea. Our review supports the 'Hopping Hotspots' model, which proposes that the locations of peak biodiversity are related to Tethyan faunai elements and track broad-scale shallow-marine habitats and high coastal complexity created by the collision of tectonic plates. A null hypothesis is the 'Whack-A-Mole' model, which proposes that hotspots occur in habitats suitable for high diversity regardless of taxonomie identity or faunai elements. Earlier 'Centre-of theories (e.g. centres of origin with diversity decreasing with distance from supposed areas of exceptionally high rates of speciation, for which easy connection to adjacent regions to the east and west is important) were based on the analysis of recent biotas with no palaeontological foundation, and may better explain diversity dynamics within a hotspot rather than those between hotspots. More recently, however, human disturbance is massively disrupting these natural patterns.