The inherent differences in baited video versus diver video survey methodologies may influence their ability to detect effects of fishing. Here the ability of no-take areas to provide sufficient protection for legal sized individuals from targeted species within the Ningaloo Marine Park (NMP) was studied using both baited remote underwater stereo-video (stereo-BRUV) and diver operated stereo-video (stereo-DOV). The relative abundance of four recreationally targeted fish species, Carangoides fulvoguttatus, Epinephelus rivulatus, Gnathanodon speciosus and Lethrinus nebulosus, were examined using both methodologies inside and outside no-take areas across the NMP. Additionally, the length-frequency distribution of the most targeted species, L. nebulosus, was investigated. Stereo-BRUVs found positive effects of protection from fishing on the relative abundance of C. fulvoguttatus, G. speciosus and L. nebulosus and larger sized L. nebulosus in no-take areas. Stereo-DOVs however did not detect any differences in relative abundance and size between areas open and closed to fishing. These contrasting results suggest that choice of sampling methodology can influence interpretations of the ability of no-take areas to provide adequate levels of protection for target species.