The influx of many organic matter changes the benthic environment in which benthic organisms inhabit. Organic matter deposited in the sediment acts as an important food source, but mass influx of organic matter affects the habitats and survival of benthic animals. Benthic animals play an important role in purifying the benthic environment and are considered as important indicators of benthic environmental disturbances. Therefore, the community characteristics of benthic animals provide quantitative information on changes in the marine benthic environment. This study investigated the environmental characteristics and the distribution pattern of benthic animals, and assessed the benthic ecosystem using Marine Biotic Index (AMBI) and Water Quality Idex (WQI) in the subtidal zone of Muan bay, southwestern coast of Korea. Sampling was conducted at 10 stations in the subtidal zone of Muan bay at summer and winter. Surface seawater was sampled using Nansen bottle, and sediment was sampled by using Van Veen grab (0.05 ㎡). The collected samples were later analyzed for water and sediment quality, and benthic animals were classified. The average of grain size was 6.21Φ at summer and 5.91Φ at winter. The grain size tended to be finer at summer than that of winter. In the upper area of Muan Bay, it showed a fine grain size composed of silt and clay, and in the lower area, it shows a corse grain size composed of sand. IL was 4.21% at summer and 4.25% at winter, showing no significant difference. The TOC was slightly higher at summer than that of winter, with 1.12% at summer and 0.78% at winter. These results showed that the upper area was finer in grain size than that of the lower area, and the organic matter content is higher. The total species number was 25 species at both summer and winter, and mean density of summer and winter were 94.90 ind./㎡ and 52.60 ind./㎡, respectively. In the upper area of Muan Bay, where the grain size was fine and organic matter content was high, annelida had dominantly appeared. However, in the lower area with coarse grain size and lower organic matter, mollusca and arthropoda were mainly appeared. WQI of Muan Bay was surveyed with an average of 23.6 (Very good; 1st grade). However, the S1 and S2 were showed an average of 37 (Moderate, 3rd magnitude) at summer. AMBI was surveyed with an average of 2.60 (Slightly polluted 2nd magnitude). However, the S2 was showed an average of 3.40 (Moderately polluted 3rd magnitude) at summer. From the cluster analysis, the benthic community was distinguished into three groups of upper, center and lower area of Muan bay. Also, the benthic community was divided into three groups by the correlation analysis with factors for benthic health assessment (WQI and AMBI). In the subtidal zone of Muan bay, there was a difference in the organic matter content according to the grain size, and it affected the distribution of benthic animals. As a result of this study, the health condition of the subtidal zone in Muan bay were good. However, from the results that benthic animals were not evenly distributed, and also the opportunistic species appeared, the load of organic matter in Muan bay seems to be increasing.