Temporal and spatial distribution in species composition and abundance of chaetognaths in relation to hydrographic variables in the waters off southern Taiwan were investigated from January 2005 to October 2006. There were 23 species of chaetognaths belonging 4 families and 12 genera recognized in this region. The 4 most dominate species were Flaccisagitta enflata (32.2%), Serratosagitta pacifica (20.6%), Zonosagitta bedfordii (12%) and Pterosagitta draco (8.8%), together comprised about 74% of total chaetognaths. The distribution in abundance of chaetognaths generally decreased from west to east along the transect, and showed clear seasonal change, with the higher abundance occurred from July to October and the lower abundance from January to May. Abundance of chaetognaths increased significantly in July 2006 and positively correlated with the abundance of copepods. Our hydrographic results indicated that South China Sea Current with higher nutrients might dominante over Kuroshio Current in this region from January 2006 to July 2006, and might lead to the increases of phytoplankton (Chl a) and copepods consequently. Furthermore, temperature and salinity also interactively influenced the distribution in abundance and species richness of chaetognaths. Stage I individuals made up the majority of chaetognaths abundance (80%). The breeding period of predominant chaetognaths (F. enflata, S. pacifica, Z. bedfordii and P. draco) are year around. Results from gut content analysis implied that copepods is the main food for chaetognaths in the study area, but the predation impact of chaetognaths on copepods was only about 0.25%¡ã2.47 %.