The semi-enclosed coastal waters of northeastern Fujian (Sansha Bay) are an important natural spawning ground for the large yellow croaker (Larimichthys crocea) in China. The yellow croaker is an important species for Chinese fisheries, and depends on a healthy zooplankton population. In this study, the seasonal succession of zooplankton in Sansha Bay was described and its relationship to the currents from the open sea was analyzed. Sampling was carried out in June, August and October 2010, and in April and May 2011. Seasonal changes in the zooplankton community structure were strongly influenced by the coastal current and the Taiwan Warm Current as well as an influx of freshwater from the mainland. A total number of 71 species of zooplankton were identified, which consisted of 19.72% warm temperate nearshore species, 30.99% subtropical nearshore species and 47.89% subtropical offshore species. In April and May, influenced by the coastal current, the water temperature and salinity were both low, which induced a bottoming-out in the diversity index (H') (2.03 and 2.02, respectively) as well as the number of species (17 and 19, respectively). The zooplankton fauna was exclusively of the warm temperate nearshore type, especially in April. Both the species number and abundance of warm temperate nearshore species were high (76.47% and 96.28%, respectively). Calanus sinicus, one of only a few dominant species in April, comprised 65.03% of the total abundance of all zooplankton. The simple structure of the zooplankton fauna comprised only a few species and with a high contribution made by each of the dominant species in this period was similar to characteristics noted in the warm-temperate water area north of the Yangtze River. During the June rainy season, a high diversity index (3.12) and species number (45) were recorded owing to the impact of the coastal current, the Taiwan Warm Current and a high volume of fresh water input. These were the most influential factors on the complex taxonomic structure and eco-group composition of the zooplankton fauna. June also displayed the highest species turnover rate, reaching up to 69.39%, compared with other months. The dominate eco-group type changed rapidly from warm temperate and subtropical nearshore species to subtropical offshore species in this month. Subtropical nearshore species comprised the highest proportion of species (73.03%). Subtropical offshore species contributed 48.89% of the overall abundance. After the rainy season, in August and October, there was a slight decrease in diversity index and species number, and the water temperature and salinity increased sharply owing to the strong affect of the Taiwan Warm Current. The zooplankton community was dominated (in terms of species numbers and density) by highly diversified subtropical offshore species. Its proportion of species number and abundance in August were 57.14% and 59.94%, respectively, and species number proportion was 57.58% in October. The community structure had many more dominant species than in April and May, of which the vast majority were subtropical offshore species. The characteristics of the zooplankton community in Sansha Bay were similar to those in the subtropical water areas of the South China Sea.