Monitoring communities of fish is important for the management and health of fisheries and marine ecosystems. Baited remote underwater video systems (BRUVs) are one of the most effective non‐destructive techniques for sampling bony fishes and elasmobranchs (sharks, rays, and skates). However, while BRUVs can sample visually conspicuous biota, some taxa are under‐sampled or not recorded at all. Here, we compared the diversity of fishes characterised using BRUVs with metabarcoding of environmental DNA (eDNA) extracted from seawater. We sampled seawater and captured BRUVs imagery from 48 locales that included reef and seagrass habitats, as well as areas inside and outside a marine reserve (Jurien Bay in Western Australia). A total of 82 fish genera from 13 orders were detected, and the community of fishes described using eDNA and BRUVs combined yielded >30% more generic richness than using either method alone. Surprisingly, rather than detecting a homogenous genetic signature, the eDNA assemblages mirror the BRUVs in being spatially explicit – there is clear differentiation of taxa between seagrass and reef habitats despite the relatively small geographical scale of the study site (∼35 km2). We show that the taxa not sampled by one approach, due to limitations and biases intrinsic to the method, can often be detected with the other. Therefore, using BRUVs and eDNA in concert provides a more holistic view of vertebrate marine communities across habitats. Both methods are non‐invasive, enhancing their potential for widespread implementation in the surveillance of marine ecosystems.