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Microbes and microbial carbonates in reef-flat and coral community dynamics and submarine geomorphologic features in reef crest and fore reef of Yongxing Island, the Xisha Islands, South China Sea, were studied by means of scuba diving, underwater investigation, and line intercept transect survey. Studies indicate a very high coral mortality with few living corals in the reef flat of Yongxing Island. Moreover, macro algae, sea grass and cyanobacteria are common in reef flat. Microbes and microbially induced carbonates occur in reef flat. Living corals grow mainly in the reef crest and fore reef, but are also declined dramatically. From coast to off shore, the southeast reef flat of Yongxing Island can be divided into beach, inner reef flat, outer reef flat, reef flat front (reef crest and fore reef), and fore-reef slope settings. Sedimentary facies include coast, reef flat, reef crest and fore reef, and fore-reef slope. Reefal carbonate sediments are composed of coral skeletons and framework, coral fragments, bioclasts, and lime mud. With the deterioration of environment and water quality, the coral communities tend to be distributed in the reef crest and fore reef with clean sea water, well circulation and moderate water energy. Reef flat is occupied mainly by the macro algae and Heliopora coerulea communities. The coverage statistics on the reef crest demonstrate that the coverage of Acropora cytherea is more than 28% and represents a dominant species with wave-resistant ecological type. Sedimentary characteristics and geomorphologic features are different between the southeast and northwest reef-flat fronts (reef crest and fore reef) of Yongxing Island. The former shows discontinuously tidal channels in outer reef flat and different dimensional and deep reef ponds in reef crest and fore reef, and the latter presents a typical spur-and-groove system. Microbes (cyanobacteria Lyngbya sp.) occur generally in the inner reef flat and reef ponds of reef crest with restricted water circulation. Widely algae growth indicates a eutrophic environment, and the common microbes on the coral surface in the reef flat and reef ponds also demonstrate eutrophication in seawater and deteriorated water quality. [ABSTRACT FROM AUTHOR]