Abstract: The Taiwan Strait is a transition zone between the East China Sea and the South China Sea with unique hydrology and a geographical environment that creates special marine community features. To analyze the spatial structure and seasonal changes of the nekton assemblages in the Taiwan Strait, seasonal experimental trawl surveys were conducted during 2006-2007. The results showed that there were two assemblages in the area with different sets of species, and the average similarity within each group varies between 39.38% and 74.20%. By using multivariate statistical analysis and analyzing the distribution of dominant species, we found that the structures of the assemblages had obvious seasonal variation. The middle region from the Putian transect to the Xiamen transect could be considered a mixing area for the two assemblages. The analysis of the relationship between species assemblages and environmental factors indicated that temperature was the most important factor affecting the community structure in cold seasons, and 22.5℃ and 17℃ could be considered dividing lines for spring and winter, respectively. In warm seasons, the most important factor was water depth, but the relationship with depth was not as significant, with a correlation between 0.264 and 0.399. The seasonal changes of nekton assemblages basically reflected the dynamic currents in the Taiwan Strait. The south coastal assemblage extended to nearly the entire area of the Taiwan Strait along with a strong and intense warm current that shrinks in spring and winter when the southward intrusion of the cold Zhejiang-Fujian coastal current becomes stronger. The impact of short-term and long-term environmental changes, such as extreme weather, global warming and human activity on nekton assemblages, had been recognized but need further research. Our study on nekton assemblages could be used as a baseline for measuring future changes.