The 2004 Asian tsunami impact on coral reefs was far from catastrophic. In most parts of the Indian Ocean destruction was very local. Pre-historic records indicate that tsunami impact on reefs can be much more dramatic. The data show that in the southern Caribbean, Holocene tsunamis completely destroyed a reef. This reef material was deposited onshore and the event caused a catastrophic phase-shift from a coral to an algae dominated ecosystem. Analyses of 4,963 coral fragments generated a distinction between tropical storm and tsunami waves as causative agents of deposition. Coral fragments (n = 45) were dated with Electron-Spin-Resonance (ESR) and radiocarbon techniques to establish a geochronology of these extreme events. Bathymetric maps of the offshore area and videography along these contours down to 30 meters depth displayed the present status of the reefs. Dating indicated four major depositional events: 4100, 3100, 1500 and 500 yrs ago. The 3D-coral reef structure did not regenerate in the last 3100 years, a time period yet undocumented in coral reef studies. A complex interaction between physical and biological factors (e.g., hurricanes and Allee effect) inhibited reef regeneration. These findings contribute to understanding the significance of extreme natural disturbances such as tsunami in coral reef ecology.