Abstract This study investigates the distributions and controls of transparent exopolymer particles (TEP) in marginal seas around Taiwan. In the euphotic zone of Kuroshio Water off southeast Taiwan, the concentration of TEP generally reached a maximum in the subsurface and then decreased with depth. The maximum concentration of TEP in every station in the Kuroshio Water coincides with the subsurface maximum of chlorophyll a (Chl. a). This implied that TEP in the euphotic zone was controlled by biological rather than physical processes. Furthermore, the ratios of TEP /POC and TEP/DOC increased with Chl. a indicating that the increase of primary production may enhance DOC transformation to POC through the formation of TEP. Concentrations of TEP in the Taiwan Strait and Gaoping coastal sea decreased generally with the increase of seaward distance, showing the same pattern of nutrient distribution. Apparently, the terrestrial input of nutrient may increase phytoplankton abundance and enhance the formation of TEP. Positive correlations were significant between TEP and Chl. a, suggesting that the distribution of TEP in the euphotic zone of Taiwan Strait and Gaoping coastal sea are also controlled by biological processes. During the study period, the concentrations of nutrient and Chl. a were elevated in the surface water around the Dongsha Island in the South China Sea (SCS), due to the influence of internal wave. According to the close relation between TEP and Chl. a, concentrations of TEP around Dongsha Island were also likely controlled by phytoplankton activity, but the different strength of internal wave may lead to the different conditions of TEP, Chl. a and POC distributions. The results of factor analysis support the fact that distributions of TEP are mainly controlled by biological processes, but various physical conditions could also influence distributions of TEP in the water column. Overall, concentrations of TEP are generally higher in the Taiwan Strait and Gaoping coastal sea than in the Donshia shelf sea and Kuroshio Water off southeast Taiwan. Nevertheless, distributions of TEP are all comparable with previous findings in other coastal and marginal seas.