We compared the community structure of reef fish over different physical complexities in 12 study zones of Bahía Honda, Gulf of Chiriquí (BH-GCH), Tropical Eastern Pacific (TEP), Panama, aiming at an analysis of the importance of the physical structure provided by corals, rocks and benthic sessile organisms. This was the first region that emerged in the Isthmus of Panama; it exhibits the oldest benthic fauna and has constant conditions in terms of temperature and salinity. Two hundred and eighty-eight visual fish censuses were conducted on 48 benthic transects from February to July 2003. One hundred and twenty-six fish species of 44 families were found. Plankton feeding pomacentrids and labrids along with haemulids that feed on mobile invertebrates were the most abundant, particularly in shallow areas. Fourteen species showed size-segregations between zones, suggesting ontogenetic migrations (smaller fishes in shallow high-complexity zones, larger-sized fishes in deeper habitats). Highly mobile and site-attached genera were abundant in most shallow, wave-exposed zones particularly on exposed rocky substrates. Planktivores were the most abundant, followed by carnivores, feeders on mobile invertebrate and piscivores. Herbivores and feeders on sessile invertebrate were lower in abundance. Species richness exceeds that of any other studied region close to the mainland in the TEP and correlates with substrate diversity, increasing size-heterogeneity of holes and structural complexity. Species diversity increases with habitat complexity and benthic diversity. It seems that water current strength, tides and waves which select for swimming, play an important role in the community organization. The study region has been proposed as a refuge-centre in the TEP, where reef fishes that evolved on coral reefs have shifted their distribution onto rocky reef habitats.