Sea urchins play an integral role in coral reef systems. As herbivores they mediate competition for space between corals and algae, as bioeroders they modify the reef substratum, and they are also a food source for some fish species. We quantified the abundance and distribution of the two most abundant sea urchin species along a fringing coral reef in Western Australia; the Ningaloo Reef. Urchin abundance was determined by evaluating 30 benthic photographs taken by divers along a 25m transect (representing an area of 10.5m2) at a total of 126 survey sites. The survey sites encompassed both outer slope and inshore reef habitats, as well as different management zones (sanctuary and non-santuary). A measure of rugosity (site structural complexity), substrate cover (percent algal cover), water velocity, and an index of predation were also determined at each survey site. Echinometra mathaei (the burrowing urchin) and Echinostrephus molaris (the mole urchin) were the two most abundant species in the study area, yet general additive models suggested that the ecological predictors that best explained the maximum variation in abundance were different for each of these two sympatric species. Echinometra mathaei abundance showed a positive relationship with food source and site structural complexity, and were more abundant in non-sanctuary compared to sanctuary zones. Interestingly, predatory fish biomass was significantly higher in these sanctuary zones. In contrast, the mole urchin, Echinostrephus molaris, was distributed predominantly on the outer reef slope, where they showed regional differences in their abundances. Since both these urchins can erode the reef through their burrowing behaviour, understanding their distribution and abundance will help to understand the role they play in shaping the reef substratum.