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The atoll reefs of the Lakshadweep, in the Indian Ocean suffered a catastrophic mortality of hard coral in the wake of the El Niño event of 1998. This study tracked changes to coral and other benthic elements in three atolls in the Lakshadweep from 2000 to 2003. The recovery of coral was highly site-specific, and appeared to be driven by differences in post-settlement survival of coral recruits, that were in turn, influenced by the local hydrodynamics of the atolls. Post bleaching recovery was highest on west-facing reefs, while recovery on east-facing reefs was very limited. However, no ‘phase-shift’ to macroalgal dominated reefs was evident. High herbivore pressures were perhaps the most important control of macroalgae. Five years after the mass mortality, the genera that showed the maximum gains represented a mix of different susceptibilities to bleaching, while some genera that were not particularly susceptible to bleaching showed significant declines. These results suggest that decline or recovery of coral is likely dependent on individual life history strategies, post-recruitment survival, and contingency.