Over recent years, many studies have identified overfishing as one of the main threats to marine fishes globally. However, studies generally focus on the effects of fishing on economically important target species and there is less information on indirect effects of fishing on non-target, reef associated fishes. Advances in remote sensing technology now offer the ability to assess these relationships over larger areas and deeper depths. Here, we use underwater remotely operated vehicles (ROVs) to identify differences in reef-associated fish assemblages between fished and unfished reefs within the Great Barrier Reef Marine Park to assess effects of fishing. We ask 1) How does diversity and abundance of reef-associated fishes differ between fished Habitat Protection Zones and unfished Marine National Parks? We also assess relationships between observed assemblages and physical characteristics of habitat, asking 2) How does reef-associated fish assemblage composition relate to habitat type and structural complexity? Results of surveys encompassing 26,600 m2 over a five-degree latitudinal gradient suggest an effect of zoning, with differences in assemblage composition between fished and unfished reefs. Managers can consider ROVs as a valued technology in this realm and future studies should continue to use them as tools to assess species and habitats.