The reefs of the Lakshadweep suffered a mass mortality of coral in 1998, in the wake of an El Niño event of unprecedented severity. In 2002, we conducted a broadscale benthic survey of six atolls in this group to check if there were geographic trends in recovery patterns across the archipelago. Four years after the mass mortality, live coral cover was relatively low on most atolls, and thin algal turfs dominated the benthos. Clear benthic differences were apparent between eastern and western aspects of reefs, pointing to the importance of local hydrodynamic conditions in determining recovery rates. Where recovery was the most apparent, it was dominated by fast-growing and bleaching-resistant coral genera. Despite the apparent lack of recovery at many sites, the reef system did not show signs of having suffered a ‘phase shift’ to a macroalgal state. High herbivorous fish abundance was likely responsible in controlling macrophyte levels, and may be crucial for further benthic recovery in these reefs.