Aim  The objective of this study was to investigate the influence of protection duration (years of fishing closure) and location (distance from shore) on reef fish diversity.

Location  Danajon Double Barrier Reef, Bohol, Philippines.

Methods  Reef fish abundance and size structure, by species, were obtained monthly using replicated underwater visual belt transects (n = 8; 70 × 5-m belt transects) over 3 years (2002–2005) at eight sites that included six marine reserves and two unprotected reef areas. We analysed species accumulation curves, diversity indices and abundance–biomass comparison (ABC) curves within and across the study sites to assess the influence of protection duration and location.

Results  Analyses showed that longer protection duration impacted reef fish diversity at both inshore and offshore sites by shifting ABC curves from higher abundance than biomass curves at fished sites to higher biomass than abundance curves at most of the protected sites. Protection duration did not significantly influence either the rate of species accumulation within sites or the 12 diversity indices measured across the study sites. The offshore sites consistently showed higher rates of species accumulation and diversity indices values than inshore sites with similar protection duration. One protected offshore young marine reserve site that has been assessed as the least well-managed showed patterns more consistent with the fished sites.

Main conclusions  Analyses showed that protection duration mainly impacted diversity by increasing the dominance of large-bodied species and enhancing total biomass. Besides protection duration, reserve location influenced species accumulation curves and diversity indices.