Inherent differences between baited remote video versus diver-operated video survey methodologies may influence their ability to detect effects of fishing. Here, the ability of no-take zones (NTZs) to provide protection for legal-sized fish from targeted species within the Ningaloo Marine Park (NMP) was assessed using both baited remote underwater stereo-video (stereo-BRUV) and diver-operated stereo-video (stereo-DOV). The relative abundance of legal-sized individuals of three recreationally targeted fish species, spangled emperor Lethrinus nebulosus, chinaman cod Epinephelus rivulatus and goldspotted trevally Carangoides fulvoguttatus, were examined using both methodologies inside and outside six NTZs across the NMP. Stereo-BRUVs found positive effects of protection on the relative abundance of legal-size C. fulvoguttatus and L. nebulosus in NTZs. Stereo-DOVs, however, did not detect any differences in relative abundances and sizes of these species between areas opened and closed to fishing. These contrasting results suggest that choice of sampling methodology can influence interpretations of the ability of NTZs to provide adequate levels of protection for target species. Our results suggest that stereo-BRUVs are a superior technique to stereo-DOVs for assessing the effectiveness of no-take zones for protection of fishery target species, reflecting bait attraction and an absence of diver influence on fish behaviour.