Cumulative anthropogenic impacts such as overfishing, and climate change are placing marine ecosystems under increasing pressure. This includes the loss or degradation of marine habitats and reductions in fish stocks, with conservation and fisheries management strategies aiming to mitigate, or reverse the effects. Measuring the effectiveness of management actions on fish requires accurate data on the abundance and size of fishes. Diver operated stereo-video systems (stereo-DOVs) have become a widely accepted method for surveying reef fish but have known biases and constraints. A new generation of small and affordable remotely operated vehicles (ROVs) can carry a stereo-video system to collect reef fish data without the need for divers. However, before ROVs are adopted there is a need to understand how they compare to other conventional survey methods. We compared how stereo-DOVs and stereo-ROVs influenced fish behaviour and sampled coral reef fish assemblages inside and outside sanctuary zones in the Ningaloo Marine Park, Northern Western Australia. In general, the numbers of species, individuals and the assemblage composition did not differ significantly between survey techniques and detected consistent patterns in the assemblage composition across locations and inside and outside sanctuary zones. Both methods recorded similar proportions of length measurements (68% and 70% for stereo-DOV and stereo-ROV respectively). Fishes were significantly more wary and exhibited more flight responses towards stereo-DOVs when compared to stereo-ROVs. The use of ROVs has the potential to be a cost-effective method of surveying reef fish while eliminating the health and safety risks involved with SCUBA diving. Given the comparable metrics as well as reduced behavioural bias and logistical advantages of using stereo-ROVs, we recommend stereo-ROVs as a viable alternative to stereo-DOVs surveys. •Fish assemblage composition sampled Stereo-DOVs and stereo-ROV was similar.•Both techniques record similar numbers of species and fish individual.•Fish allowed the Stereo-ROVs to approach them closer than stereo-DOVs.•Stereo-ROV is a cost-effective alternative to stereo-DOVs.•Stereo-ROV can operate deeper, with less health and safety risks then stereo-DOVS.