Visible lesions on coral colonies are potential indicators that environmental stressors are influencing a reef. To test this hypothesis, pairs of near-shore reefs on Taiwan were surveyed along an anthropogenically influenced gradient that included locations near the cities of Taipei and Taitung, and more remote reefs off Green Island. Two fringing reefs at Sanya, Hainan Island, a popular Chinese resort area, were also assessed. Field surveys were undertaken to detect, quantify and visually describe the occurrence of lesions at each site. Coral mucus samples were collected from both normal-appearing polyps and lesion-afflicted areas of colonies to assess carbon requirements of associated microbes. Tissue samples were also collected to identify bacterial communities inhabiting healthy tissue for comparison with those associated with lesions; denaturing gradient gel electrophoresis and 16S rRNA sequencing for bacterial identification were utilized in these analyses. In addition, tissue samples were collected in the vicinity of lesions and prepared for histological examination. At sites in Taiwan, lesions were encountered twice as often at the sites near Taipei and Taitung than at Green Island. The fewest (15/72 sightings) lesions were encountered at the reefs near Sanya, primarily because there has been nearly an 80% loss of coral cover at Sanya in recent decades. Overall, tissue loss was the most common lesion recorded (52%), followed by pink discoloration (27%) and color loss (i.e., bleaching, 15%). Porites was the taxon most commonly observed with one or more lesions (45% of sightings). Microbes within mucus from lesioned areas utilized similar carbon sources as microbes from mucus from healthy polyps, but utilized those sources more than twice as often. Examples of carbon sources utilized by microbes in >50% of the lesion samples were D-cellobiose, D-mannitol, N-acetyl-D-glucosamine, alpha-cyclodextrin, and glycogen. Bacterial assemblages on corals were significantly different between Taiwan and China, among sites, and between water samples and coral samples, but not between healthy samples and lesions. Bacterial sequences identified in tissue samples from lesions revealed the presence of well-known disease-related genera, such as Clostridium and Vibrio. Microbes specifically indicating anthropogenic sources, included Bacillus sp. (sewage sludge) and Geobacillus thermolevorans (irritable bowel syndrome). Histological examination of tissue samples, particularly those from lesions characterized as tissue loss, revealed fragmentation and detachment from the mesoglea of gastrodermis and epidermis, as well as brown granular material, and the presence of ciliates and small crustaceans. Corals are susceptible to a variety of diseases. For reefs in the western Atlantic and Caribbean, occurrences of lesions and characterization of coral diseases have been relatively well documented. In contrast, many areas in the vast Indo-Pacific, including the reefs of Taiwan and China, have received much less attention. This study of lesions and associated microbiomes on nearshore reefs of Taiwan and Hainan Island supports previous research that has revealed higher incidences of coral lesions and disease in reefs near extensive human populations. The results also support the hypothesis that many of the microbes associated with coral lesions are part of the natural coral microbiome and that some microbes can become opportunistic when the host corals are stressed.