Habitat complexity plays a major role in determining the distribution and structure of fish assemblages in the aquatic environment. These locations are critical for ecosystem function and have significant implications for conservation and management. In this study, we evaluated the utility of remotely sensed lidar (light detection and ranging) data for deriving substrate rugosity (a measure of habitat complexity) on a coral reef in Hawaii. We also assessed the potential application of lidar data for examining the relationship between habitat complexity and Hawaiian reef fish assemblage characteristics. Lidar-derived rugosity (4 m grid size) was found to be highly correlated with in-situ rugosity and was concluded to be a viable method for measuring rugosity in analogous coral reef environments. We established that lidar-derived rugosity was a good predictor of fish biomass and demonstrated a strong relationship with several fish assemblage metrics in hard bottom habitat at multiple spatial resolutions. This research demonstrates (i) the efficacy of lidar data to provide substrate rugosity measures at scales commensurate with the resources and their environment (ii) the applicability of lidar-derived rugosity for examining fish–habitat relationships on a coral reef in Hawaii and (iii) the potential of lidar to provide information about the seascape structure that can ultimately be used to prioritize areas for conservation and management.