This study was based on samples taken from 7 cruises between February 2004 and November 2004 and intended to investigate the effects of hydrographic conditions on the spatiotemporal variations of fish larvae assemblage in the waters surrounding Taiwan. The cold, low salinity, and nutrient-rich waters were usually found in the seas northwest of Taiwan in winter, probably due to the invasion of China Coastal Current (CCC). While the dominance of warm and saline waters in the Taiwan Strait in summer and in the waters south and east of Taiwan throughout the year implied that the waters of these areas might be controlled by Kuroshio Current (KC) and South China Sea Waters. In total, 622 fish larvae taxa belonging to 295 genera and 138 families were identified by this study with an overall mean abundance of 760.52 ¡Ó 75.63 ind./1000m3. No significant difference in abundance was found among seasons. The 10 predominant taxa, which constituted 32% of the total number of fish larvae, were Engraulis japonicus, Benthosema pterotum, Scomber japonicus, Vinciguerria nimbaria, Encrasicholina punctifer, Sigmops gracilis, Auxis sp., Trichiurus lepturus, Bleekeria mitsukurii, and Maurolicus sp.. The distribution patterns of fish larvae showed a close relationship with the water masses, higher abundance and lower species richness of fish larvae were always found in the northwestern and northern waters of Taiwan where the CCC prevails, and lower abundance and higher species diversity were present in the eastern waters of Taiwan where the KC dominates. Results of cluster analysis distinguished three station groups, the western, transitional, and eastern groups, and the distribution patterns of these station groups were also corresponded with hydrographic conditions. Furthermore, two seasonal groups of fish larvae assemblages were also recognized, spring-summer group and autumn-winter group. Results of correlation coefficients showed that total abundance of fish larvae and the most dominant taxa were positively related to zooplankton abundance but negatively related to phytoplankton abundance, and suggested that food source might be a key factor to determine the abundance and distribution of fish larvae in the waters surrounding Taiwan. Results of indicator species analysis designated Engraulis japonicus the indicator species of the CCC, and Vinciguerria nimbaria, Maurolicus sp., and Sigmops gracilis the indicator species of the KC.