The cyclone Erica (Class 5) hit the South Lagoon Marine Park of New Caledonia on 14 March 2003, in the midst of a survey conducted on coral reef fish and habitat of Larégnère and Crouy reefs. Such perturbation was exceptional for the area. Nine stations had already been sampled (8–11 March 2003) when the cyclone hit the reefs. These stations were sampled again just after the cyclone (23 March–15 April 2003) and 20 months later (14–16 November 2004). Erica had a significant initial impact on habitat characteristics. The fragile coral forms cover (branching, tubular and foliose) decreased significantly, resulting in a loss of habitat for the fish communities. Species richness and biomass of the commercial reef fish and the Chaetodontidae decreased just after Erica, but not the density. The species assemblage was modified on the stations with the lowest remaining live coral cover. The loss of shelter modified the behaviour of potential prey, which constituted unusual shoals and attracted predators. Twenty months after Erica, the habitat had not recovered and the broken coral colonies were transformed into rubble or colonized by algae. The nature of the mid-term impact on the fish communities was different and more significant than the initial impact. Species richness per station, density and biomass were significantly lower than before and just after Erica. This pattern was confirmed for all the main families, with the exception of Acanthuridae. A different fish assemblage was observed on all stations 20 months after Erica. Herbivorous species and benthic macro-invertebrate feeders associated with rubble replaced the coral associated species that characterized the assemblages before the cyclone. When a Class 5 cyclone affects an area where perturbations of such intensity are uncommon, its impact is immediate and the mid-term consequences are even more significant. A complete modification of the structure of the habitat and the fish assemblages is observed. The consecutive recovery should be a long process.