Until recently, the only examples of inverted biomass pyramids have been in freshwater and marine planktonic communities. In 2002 and 2008 investigators documented inverted biomass pyramids for nearly pristine coral reef ecosystems within the NW Hawaiian islands and the Line Islands, where apex predator abundance comprises up to 85% of the fish biomass. We build a new refuge based predator-prey model to study the fish biomass structure at coral reefs and investigate the effect of fishing on biomass pyramids. Utilizing realistic life history parameters of coral reef fish, our model exhibits a stable inverted biomass pyramid. Since the predators and prey are not well mixed, our model does not incorporate homogeneous mixing and the inverted biomass pyramid is a consequence of the refuge. Understanding predator-prey dynamics in nearly pristine conditions provides a more realistic historical framework for comparison with fished reefs. Finally, we show that fishing transforms the inverted biomass pyramid to be bottom heavy.