This work is a part of the Taiwan Cooperative Oceanic Fisheries Investigation, the first large scale hydrographic and plankton survey around Taiwan (21-26°N, 119-123°E). The present study examined the influence of hydrodynamic and biological variables driven by monsoon system on the siphonophore assemblages through an annual cycle in 2004. Calycophorans, namely Chelophyes appendiculata, Diphyes chamissonis, Lensia subtiloides, Bassia bassensis, and Muggiaea atlantica, were the most dominant siphonophore species. Maximum abundance of these dominant species generally occurred during the warm period (May and August), while M. atlantica had a significantly peak abundance in February. Although no apparently temporal difference in siphonophore abundance was observed in the study, siphonophore assemblage was more diverse in August than in other sampling times. Result of a cluster analysis indicated that assemblage structure of siphonophores in the waters around Taiwan varied at temporal and spatial scales during the sampling period. The intrusions of the Kuroshio Branch Current and China Coastal Current to the study area play an important role on the transportation of siphonophores. Also, the distribution of siphonophore assemblage was closely related to the hydrographic characteristics, with temperature, chlorophyll a concentration, and zooplankton abundance being the major environmental factors affecting the spatio-temporal variability of siphonophores. This study contributes substantially to the new knowledge of the siphonophore assemblage in the tropical-temperate waters of Taiwan.