The ability of local communities to sustainably manage natural resource harvests in coral reefs ecosystem depends heavily on the strength of traditional institutions. Coastal communities have evolved a suite of restrictive practices to control marine offtake and there is considerable recent evidence of their effectiveness in protecting and enhancing resource stocks. However, traditionally imposed restrictions can vary considerably in their complexity and in their functional effectiveness. The indigenous communities of the Nicobar Islands are dependent on marine resources for sustenance, managing them with a range of traditionally imposed restrictions. These include limited entry to certain locations, closed seasons and areas, and restrictions on species, size-classes of fish and fishing methods. We tested the relative effectiveness of protection in areas managed under different traditional control regimes by comparing the abundance and biomass of targeted fish groups in managed and unmanaged areas. Our results indicate that reef sites with the strictest form of restriction e essentially no-go areas e had significantly higher abundance and biomass values of most functional groups of fishes compared with partially protected and control locations. In contrast, targeted food fish stocks did not differ from control locations in partially protected sites managed with even complex forms of traditional management. Ensuring that traditional harvest rules are complied is critical to the success of any management system, and our results suggest that they can be most strictly enforced in traditional no-go areas. Our work highlights the importance of critically evaluating the factors influencing traditional management systems to strengthen their ability to protect these reefs from unsustainable overharvest.