Tuya, F. C., Soboil, M. L., and Kido, J. 2000. An assessment of the effectiveness of Marine Protected Areas in the San Juan Islands, Washington, USA. – ICES Journal of Marine Science, 57: 1218–1226. Marine protected areas (MPAs) can serve as effective sites for sheltering targeted populations. Furthermore, populations can experience increased abundance and body size in such areas. In this study we compared the abundance and body sizes of commonly collected fish and invertebrate species inside three marine preserves established eight years prior to our survey (University of Washington marine research preserves), two newly established MPAs, and three unprotected sites in the San Juan Archipelago. To determine whether population abundance and individual size were greater in protected areas within each site, these two parameters were measured for the red urchin (Strongylocentrotus franciscanus; Agasizz, 1865), sea cucumber (Parastichopus californicus; Stimpson, 1857), scallops (Chlamys rubida; Hinds, 1845; Chlamys behringiana; Midendorff, 1849; Hinnites giganteus; Gray, 1825), copper rockfish (Sebastes caurinus, Richardson, 1845), quillback rockfish (Sebastes maliger, Jordan & Jilbert, 1880), China rockfish (Sebastes nebulosus; Ayres, 1854) and lingcod (Ophiodon elongatus; Girard, 1854). The newly established MPAs and unprotected sites showed similar levels of abundance and size frequency distributions for the target species. Differences in abundance and size of small red urchins, scallops, rockfishes, and lingcod were not found among the three categories of sites, which could be attributable to a lack of effective protection within the protected sites. The UW marine preserves exhibited greater abundance of medium and large sized red urchins, which is explained because these areas lie within an urchin fishery closure zone established in the late 1970s. Ordination techniques showed that fishing pressure was the main cause of the decreased target populations assemblages. This study suggests that marine preserves have been effective in enhancing the medium and large size classes of the red urchin populations. 2000 International Council for the Exploration of the Sea