In three oceanographic surveys conducted in the coastal waters of central Fujian Province (24°55'-25°13' N, 119°11'-119°32' E) in December 2009 and April and August 2010, the abundance, biomass, horizontal distribution, and seasonal variation of zooplankton were investigated, and their relation to the seasonal variation of water masses in the Taiwan Strait was examined. The results showed that the numbers of zooplankton changed between winter and spring, but remained steady between spring and summer. In winter and spring, the zooplankton showed similar patterns of distribution, though the distribution pattern was different in summer. The average number of zooplankton was 8.90 ind./m³ in winter and 245.65 ind./m³ in spring. In these two seasons, the zooplankton were most abundant in nearshore waters and gradually diminished offshore. In summer, the average number of zooplankton was 236.82 ind./m³. The zooplankton abundance in nearshore waters was low, but the zooplankton were abundant in offshore waters. To ascertain which species made the greatest contribution to these distribution patterns, the regression contribution of each dominant species' abundance was computed. In winter and spring, Calanus sinicus was the species whose distribution determined the distribution of zooplankton abundance. In summer, Lucifer hanseni and Diphyes chamissonis exerted the greatest influence on the distribution of zooplankton abundance. As a warm-temperate species, Calanus sinicus usually prospers in low-temperature waters. By contrast, Lucifer hanseni and Diphyes chamissonis are warm-water species; they are usually abundant in high-temperature waters. The adaptability of these three species to water temperature is an important factor in determining the distribution patterns of zooplankton abundance in each season. However, the most important factor is the seasonal variation of the water masses in the Taiwan Strait. This variation leads to the seasonal alternation of the dominant species. In winter, the west side of the Taiwan Strait is controlled by China's coastal water, which has a low temperature. The dominant species in the investigated waters in winter were warm-temperate species like Calanus sinicus. In spring, as the northeast monsoon weakens, China's coastal water wanes and the Taiwan Warm Current becomes stronger. However, the west side of the Taiwan Strait is still controlled by China's coastal water so warm-temperate species are still dominant. In winter and spring, the offshore water has a relatively high temperature because of the Taiwan Warm Current. Correspondingly, in the offshore water Calanus sinicus had a low abundance. The greatest abundance of Calanus sinicus was in the nearshore water. In summer, the southwest monsoon begins and the Taiwan Warm Current dominates. The major species were mainly warm-water species, such as Lucifer hanseni and Diphyes chamissonis. In summer, the water is heavily stratified, and there is an upwelling of bottom water in the nearshore region of the western side of the strait. As a result, the water temperature in this region was the lowest. Accordingly, warm-water species such as Lucifer hanseni and Diphyes chamissonis, were less abundant in the nearshore water. The different distribution patterns of these important zooplankton species further influenced the total abundance and overall distribution patterns in different seasons.