A major focus of paleoecological studies is to disentangle human influences from natural ranges of variability in living marine resources. Previous historical analysis demonstrates a massive decline and extinction of exploited species in tropical marine environments, but it was unclear whether there was any general pattern in the decline. Here I present results from a time-series analysis of the condition of the marine biota (megafauna and architects) from 13 coral reef sites from around the world using a consistent analytical framework. Components of the marine megafauna include large and small carnivores and herbivores, and that for the architects include corals, seagrasses and suspension feeders. The state of marine megafauna and architect populations was assessed at seven different time intervals from pre-human (40,000 ybp) to 2000 AD. The six faunal states range from 'pristine' to 'globally extinct'. The results demonstrate a clear trajectory of decline in all major ecosystem components of tropical coastal communities. The pattern of decline happens everywhere in the same sequence, but not synchronously, with some locations ahead of others, and varies among ecological groups. Overfishing at multiple levels of the food chain has not only resulted in the closure of fisheries, but also in dramatic and so far irreversible phase changes in the benthic communities. Our analyses demonstrate that for all of the study areas, including the Great Barrier Reef, present activities of use are not sustainable and haven't been for some period back in time.