The effect of recreational SCUBA diving on coral reefs is likely secondary to many of the commonly cited stressors that threaten the long-term survival of coral reefs, such as rising temperatures. However, recreational SCUBA diving has had documented effects on various benthic organisms. Most research on the effect of SCUBA divers has focused on broken and abraded benthic organisms or the rate at which divers contact the benthos. We tested for differences in the structural complexity and benthic assemblage between pairs of heavily and lightly trafficked dive sites in Bonaire, a popular Carribbean diving destination. There was roughly 10 % less structural complexity in areas of heavy traffic. This is alarming given that the structural complexity of shallow reefs in Bonaire is substantially lower than in the 1970s. Different functional groups of benthic organisms were affected differentially by diving traffic. For instance, massive corals such as Orbicella annularis were 31 % less abundant at heavy than light diver traffic areas, while gorgonians and sponges had similar abundances at heavy and light diver traffic areas. Our results match those of previous studies on the resistance and resilience of tropical benthic reef organisms to physical disturbances that suggest that stony corals are more prone to physical damage than gorgonians and sponges. We provide a number of possible management strategies that could reduce the effects of recreational SCUBA divers on Bonaire and elsewhere, including education/intervention by dive guides and concentration of diving traffic away from areas of stony coral abundance.