bioRxiv: No-take marine reserves (NTRs), i.e. areas with total fishing restrictions, have been established worldwide aiming to provide biodiversity and ecosystem conservation. Brazil has established NTRs, but currently lacks scientific knowledge and understanding of their ecological role, particularly regarding rocky reefs in subtropical regions. Consequently, this study aimed to contrast NTR, from the 30 year old Tupinambás Ecological Station, and comparable fished sites across a coastal biogeographic gradient to investigate the effect of fishing and habitat variability on the abundance and body-size of rocky reef fish. We used Baited Remote Underwater stereo-Video (stereo-BRUVs) and Diver Operated stereo-Video (stereo-DOVs) systems to simultaneously sample reef fish and habitat. Model selection and results identified habitat and biogeographic variables, such as distance from shore, as important predictor variables, explaining several aspects of the fish assemblage. The effect of protection was important in determining the abundance and body-size of targeted species, in particular for epinephelids and carangids. Conversely, species richness was correlated with habitat complexity and not with protection status. This is the first study to publish data using these novel survey methods in the Southeastern Atlantic and demonstrate their utility, in combination with an established network of NTR’s, to provide benchmarks for conservation and fisheries management.