Information regarding the vagile fish fauna and their use of rare polychaete reefs as habitat or feeding area is almost unheard of in the tropics. Of great interest is whether the construction of such biogenic reefs in an otherwise featureless habitat such as a mudflat increases structural complexity thereby enhancing fish abundance and ecological functioning. The Jeram polychaete reef (Straits of Malacca) is unique and recurrent; on the mudflat, it emerges, grows, and decimates within a year. We tested the hypothesis that the enhanced reef resources (prey) modify the reef ichthyofauna in terms of community structure and trophodynamics. The largely juvenile fish that visited the reef totaled 69 species from a 9-month study. Although sharing 57 common species, the reef fish assemblages had less species and diversity than the mudflat (90 species) and also lower abundance and biomass. Temporal variability in the reef’s fish community structure appeared to be tied to the reef dynamics, food availability, and environment. Stable isotope (C and N) results suggest a food web of five trophic levels emanating from phytoplankton and benthic diatoms as basal sources, similar to the mudflat. The enhanced prey resources modified the ichthyofauna, but did not impact reef fish trophodynamics in terms of feeding guild, trophic level, and dietary carbon. Although the polychaete feeding guild was distinct in the reef, most reef fishes as well as mudflat fishes were generalist predators. The reef supports local fisheries, functioning as a feeding and habitat area for 58 fish species of commercial importance.