Background: The mesoscale distribution of thaliaceans associated with hydrographic conditions in the waters around Taiwan was investigated during two different monsoon seasons in 2004 in order to elucidate possible influences of hydrological conditions driven by seasonal monsoons on distributional patterns of thaliaceans. Results: In total, 18 thaliacean species, belonging to 12 genera and 3 families, were identified in our samples. Thalia rhomboides, Doliolum denticulatum, Doliolum nationalis, Thalia orientalis, Pyrosoma verticillatum, and Thalia democratica were the six predominant species and contributed 93% to the total thaliacean collection by number. Thaliacean assemblages were similar in composition between seasons, but abundances and species numbers were higher in summer than in winter. Spatial distribution patterns of doliolids and salps clearly differed and were closely associated with hydrographic characteristics. Doliolids were mainly found in lower-salinity and nutrient-rich shelf and neritic waters; among them, D. denticulatum could be used as an indicator species of the China Coastal Current. Most salp species showed higher abundances in warm oceanic waters, such as the Kuroshio Current, Kuroshio Branch Current, and South China Sea Surface Current.Conclusions: This study showed that the succession of water masses driven by monsoons affects seasonal and particularly spatial distributions of abundances of the thaliacean assemblage in the area studied.