The analyses of diversity of nekton in Dongshan Bay and adjacent areas were carried out based on the data of bottom surveys from November 2009 to August 2010. A systematic analysis of the nekton species composition was studied, and the index of relative importance (IRI), relative resource density, Margalef richness index, Shannon-Weiner diversity index and Pielou evenness index were employed to assess the diversity of nekton. Also the spatial-temporal pattern of the nekton species in this area was described. The results showed that there were a total of 168 species involving 20 orders, 74 families and 109 genera in Dongshan Bay and adjacent areas. There were 114 fish species which was the largest category, accounting for 67.86%, and the results were shown the same trend compared with that of Taiwan Strait. In term of seasonal distribution, the most abundant of species was in spring (95) and least in autumn (66); in term of the spatial distribution, the survey station 9 in summer had the largest number of nekton species (37), while the survey station 3 had the least number (5) in the spring. The relative resource densities of spring and autumn were the higher, with winter the lowest and summer moderate. Dominant species had relatively less number of species, no more than four species, the number of dominant species in spring, summer, autumn and winter was 4, 2, 1 and 3 respectively. Dominant species were quite different and there was an obvious seasonal fluctuation. The level of diversity index indicated summer spring autumn winter. In term of the seasonal distribution, the average values of Margalef richness index, Shannon-Weiner diversity index and Pielou evenness index were 3.54, 1.99 and 0.71 respectively. In term of the spatial distribution, the average values of Margalef richness index, Shannon-Weiner diversity index and Pielou evenness index were 7.87, 2.94 and 0.75 respectively. Biodiversity of nekton in the area was at a low level, which was mainly due to over-fishing, water pollution and other comprehensive factors. This study could provide a scientific basis for marine construction, evaluation of fishery resources, marine ecological restoration, ecosystem-based fisheries and marine management strategy.