BackgroundAssessing fish assemblages in subtidal and intertidal habitats is challenging due to the structural complexity of many of these systems. Trapping and collecting are regarded as optimal ways to sample these assemblages, but this method is costly and destructive, so researchers also use video techniques. Underwater visual census and baited remote underwater video stations are commonly used to characterise fish communities in these systems. More passive techniques such as remote underwater video (RUV) may be more appropriate for behavioural studies, or for comparing proximal habitats where the broad attraction caused by bait plumes could be an issue. However, data processing for RUVs can be time consuming and create processing bottlenecks.MethodsHere, we identified the optimal subsampling method to assess fish assemblages on intertidal oyster reefs using RUV footage and bootstrapping techniques. We quantified how video subsampling effort and method (systematicvsrandom) affect the accuracy and precision of three different fish assemblage metrics; species richness and two proxies for the total abundance of fish, MaxNTand MeanCountT, which have not been evaluated previously for complex intertidal habitats.ResultsResults suggest that MaxNTand species richness should be recorded in real time, whereas optimal sampling for MeanCountTis every 60 s. Systematic sampling proved to be more accurate and precise than random sampling. This study provides valuable methodology recommendations which are relevant for the use of RUV to assess fish assemblages in a variety of shallow intertidal habitats.