The coral reefs and associated ecosystems of Cayos Cochinos, Honduras were briefly surveyed in early May 1995. The north coasts of the larger islands are exposed to greater wave energy and the reefs, dropping steeply to sandy slopes at approximately 30m, were dominated by often massive colonies of the various forms of Montastraea annularis commonly forming ramparts. The reefs surrounding the tiny carbonate islands in the lee were dominated by Agaricia tenuifolia and were more diverse in coral species. The shallow shelf extending towards the mainland 25 km to the west had scattered A. tenuifolia patch reefs, sand lenses, and sea grasses. There were extensive beds of sea grasses dominated by Thalassia testudinum and Syringodium filiforme to the south east and south west of Isla Cochino Pequeno. Benthic algae, primarily the brown algae Dictyota spp. and Lobophora variegata, were abundant at all sites surveyed, sometimes over-growing living corals. Algal abundance was highest nearest to dense human populations. The most likely human disturbances are over-fishing and nutrification, perhaps acting in synergy with periodic storm damage. The Cayos Cochinos Biological Reserve will be an important experiment on the impact of fishing and other human disturbances on the balance of corals and algae on coral reefs.