Areas closed to fishing are advocated as both fisheries management and biodiversity conservation tools. However, few studies investigate the responses of suites of both target and non-target fish species within an assemblage, which is an important consideration for ecosystem-based fisheries management approaches. Diver-operated stereo-video was used to assess the abundance and length of coral reef fish across multiple areas both open and closed to fishing at the Houtman Abrolhos Islands, Western Australia. After taking into consideration spatial differences in benthic habitat, the composition of fish assemblages was found to differ between open and closed areas. The target species, Plectropomus leopardus, was approximately two times more abundant in closed areas. Furthermore, 51 % of P. leopardus were larger than the minimum legal length (MLL) for retention in closed areas compared with only 1.8 % in areas open to fishing. Another target species, Choerodon rubescens was surveyed in greater abundance at sizes larger than the MLL in closed areas (64 % >400 mm) in comparison with areas open to fishing (36 %). A number of non-target species were also larger in closed areas (e.g., Kyphosus cornelii, Scarus schlegeli). In contrast, several non-targeted prey species were more abundant in open areas (e.g., Pomacentrus milleri was six times more abundant in open areas). Our results document complex responses of target and non-target species in closed areas at the Houtman Abrolhos Islands. © 2014 Springer-Verlag Berlin Heidelberg.