Biodiversity of coral reef fish species is often related to the structural complexity and diversity of their habitats. This study explores the relationship between fish species richness, habitat diversity (substrate diversity) and habitat complexity (rugosity). Habitat diversity and topographic measures were used to predict reef fish diversity. It was hypothesized that high fish species diversity would show a positive correlation with greater habitat structure, which includes habitat diversity and topographic complexity. Fish species richness was determined at six dive sites in Bonaire, N.A. (Karpata, Andrea II, Cliff, Windsock, Angel City, and Red Slave) using data from 20 randomly chosen expert-level surveys provided by Reef Educational Environmental Foundation (REEF) for 2004 – 2009. Preliminary analysis of REEF data was used to select sites with high and relatively low fish species richness to make comparisons with the habitat structural complexity measurements (substrate diversity and rugosity). Substrate diversity and habitat complexity were measured using a 10 m transect randomly placed at 4 depths (2, 6, 12, and 18 m) at each site. Substrate diversity was determined by measuring the percent cover of the different substrates and then using the Shannon Diversity Index to determine H’. The rugosity of the sample area was measured by fitting a lead line to the reef at each of the determined depths. Overall results suggested that topographical complexity (rugosity) was not related to high fish species richness at dive sites on Bonaire. There was a weak positive correlation between H’ and fish species richness on the reef slope and a weak negative relationship between H’ and fish species richness on the reef flat. The results provide evidence that there are more factors to consider when explaining fish species richness on coral reefs than the structural complexity of the habitat at the scale of this study.