Traditional fishery resource assessment methods using trawl gear are unable to sample rocky substratum and are prone to underestimating the biomass of species having partial or strong association with rocky reefs. This study successfully used an Autonomous Underwater Vehicle (AUV) and image-yielding methods to estimate size, abundance and habitat preference of an abundant and commercially important ‘rockfish’ – the Ocean Perch (Helicolenus percoides) – in rocky habitats on the continental shelf off Tasmania, SE Australia. More than half (53%) of the Ocean Perch observed were photogrammetrically measured with known accuracy using a stereo camera system yielding length-frequency distributions. Observations of juvenile and adult H. percoides across a depth gradient showed that adults preferred rocky substrates over soft substrates, whereas juveniles preferred soft substrate over hard substrate. We found a positive relationship between rockfish abundance and increasing depth in most habitat types. These results demonstrate the utility of image-based methods for determining size composition and habitat preferences of some reef-associated species. However, there is scope to improve image-based methods using length estimation procedures that enable higher proportions of individuals to be measured (compared to the proportion achieved in this study), and by incorporating automated image annotation to decrease image analysis times, particularly when examining species/habitat relationships. The importance of analytical procedures that account for autocorrelation in non-independent image data on habitats and associated species is discussed. We conclude that rapidly maturing image-based observational methods have potential utility in complementing fishery stock assessments of some reef-associated species. Image-based methods are also well-suited to simultaneously provide additional quantitative measures of benthic habitats, invertebrate fauna and fishery environments.