Thirty-five species of chaetognaths belonging to fourteen genera and four families were identified in the waters of southwestern Taiwan from July 2009 to April 2010. In surface tows, thirty-five species of chaetognaths belonging to fourteen genera and four families were found, with mean abundance of 2911 ¡Ó 586 ind./ 100m3; in oblique tows, thirty species of chaetognaths belonging to fourteen genera and four families were identified, with mean abundance of 3180 ¡Ó 532 ind./ 100m3. The five predominant species were Flaccisagitta enflata, Aidanosagitta regularis, A. neglecta, A. delicate and Serratosagitta pacifica, together they constituted 72 % of the total catch. The hydrographic conditions in the waters southwestern Taiwan were affected by seasonal monsoons and water masses. Higher temperature, lower salinity, and higher nutrient concentration were found in summer, and lower temperature, higher salinity, and lower nutrient concentration in winter. Generally higher abundance of chaetognath was found in summer and in inshore waters, and lower in spring and in offshore waters. Furthermore, the abundance of chaetognath showed significantly positive correlation with copepods, but no significant correlation with temperature and salinity. The predominant chaetognaths were mostly stage I (47 ~ 89 %), adult stage(>stage III) was mainly found in April. The average body lengths (ABL) of Fl. enflata, A. regularis, A. delicate and Se. pacifica were larger in spring than in summer, while the ABL of A. neglecta exhibited larger in winter than in summer and autumn. This study implies that the distribution of weight mean stage (WMS) and ABL of chaetognath were likely influenced by the water masses, because the ABL of Fl. enflata and WMS of Se. pacifica were larger in high salinity waters, furthermore, this study found that the seasonal moonsons and the succession of water masses maybe played important factors in the distribution patterns of chaetognaths.