Sea urchins can play a critical ecological role in the functioning of marine benthic ecosystems, mediating competitive interactions between corals and algae. Yet, little is known about factors affecting urchin distribution in intact coral reef systems. This study aims to determine the spatial distribution of two sympatric urchin species, Echinometra mathaei and Echinostrephus molaris, and potential factors contributing to this, within the intact coral reef system of Ningaloo Marine Park, north-western Western Australia. Benthic photographs and surveys were conducted on SCUBA at 126 sites across the Park to determine urchin presence, rugosity, substrate cover, water velocity, and fish predation for each site. Generalised additive models found that E. mathaei presence was positively related to algal cover, rugosity and non-sanctuary zones, suggesting that distribution may be driven by foraging behaviour, habitat complexity and predation. Echinostrephus molaris presence was positively related to habitat and region, suggesting its distribution may be largely driven by hydrodynamics, feeding strategy and regional variation. This study highlighted species-habitat associations and the complexities of these in structuring urchin communities. Although occupying similar niches, the predominantly non-overlapping feeding preferences, and morphological and behavioural differences between E. mathaei and E. molaris enable these species to coexist within the intact reef system of Ningaloo Marine Park.