1. Marine protected areas (MPAs) range from multiple-use areas (MUA) to absolute no-take reserves (NTR). Despite their importance for fisheries management, there are few long-term studies comparing benefits from different types of MPAs within the same region. 2. Fish assemblages were monitored for five years (2001-2005) in the largest coral reefs in the South Atlantic (Abrolhos Bank, Brazil). Monitoring included one community-based MUA two NTRs (one established in 1983 and another in 2001), and one unprotected area. Benthic assemblages at these areas, as well as fish assemblages on unprotected deeper reefs (25-35 m), were monitored from 2003 onwards. 3. Habitat characteristics strongly influenced fish assemblages' structure. This, together with the lack of data from before establishment of the MPAs, did not allow an unequivocal analysis of the effects of the MPAs. 4. Biomass of commercially important fish, particularly small carnivores, was higher in the older NTR. Biomass of black grouper Mycteroperca bonaci increased by 30-fold inside NTRs during the study period, while remaining consistently low elsewhere. 5. A single herbivore species, the parrotfish Scarus trispinosus, dominated fish assemblages (28.3% of total biomass). Biomass of this species increased in 2002 on the younger NTR and on the MUA, soon after establishment of the former and banning of the parrotfish fishery in the latter. This increase was followed by a decline from 2003 onwards, after increased poaching and reopening of the parrotfish fishery. 6. Fish biomass increased in 2002 across the entire region. This increase was stronger in sites closer to deeper reefs, where fish biomass was up to 30-times higher than shallow reefs: movement of fish from deeper to shallower areas may have played a role. 7. The effective use of MPAs in the Abrolhos Bank is still dependent on adequate enforcement and the protection of critical habitats such as deep reefs and mangroves. Copyright (c) 2008 John Wiley & Sons, Ltd.