A unique assemblage of tropical and temperate marine organisms characterizes the Houtman Abrolhos Islands, four clusters of islands and reefs off the coast of mid-Western Australia. Four reef observation areas or marine protected areas (MPAs) were established in 1994 to examine their value in protecting vulnerable reef fish species, including the sub-tropical wrasse, Choerodon rubescens, and the coral trout, Plectropomus leopardus. In 1993 and 1994 (prior to protection), population densities and body sizes were monitored at two island groups (Easter and Wallabi). At each location, the MPAs and the equivalent ‘control’ areas to remain open to fishing were monitored by underwater visual censuses. These closed and open areas were subsequently monitored four more times between 1995 and 2002 to assess long-term trends in abundance and population structure. Populations of the wrasse, C. rubescens, did not appear to respond to protection, exhibiting irregular fluctuations in both closed and open areas throughout the study. In contrast, although there were no significant increases for P. leopardus for the first three years of closure, after eight years of protection there were significantly larger numbers of P. leopardus in the closed areas. There was a three-fold increase at the Easter Group and a seven-fold increase at the Wallabi Group, relative to open fishing areas, attributed primarily to reduced fishing mortality. Significant closed areas (17% of the P. leopardus habitat) provided substantial stock-wide impacts. The data also indicate that the MPAs can be effective where some forms of fishing (such as lobster fishing) are permitted which are compatible with the objectives of the MPA. While MPAs are clearly an effective tool for increasing the local abundance of some reef fishes, the spatial and temporal scales required for their success may vary among species.