To clarify the spatio-temporal variations of larval fish assemblages in the northeastern waters of Taiwan, fish larvae were collected from 36 and 38 predesigned stations by using Bongo or ORI nets on R/V Hai-Chieng during June and July 2005 and August and September 2006, respectively. Temperature and salinity of water column, and the water volume being filtered during sampling tow were also measured. A total of 4,819 individuals of larval fish belonging to 76 families and 183 taxa were identified. The predominant species were Auxis sp. (June, 2005), Benthosema pterotum (July, 2005) and Engraulis japonicus (August and September, 2006). There were 6 assemblages of larval fishes in each month. Water temperature and salinity in the 10 m depth could be used as an indicators to identify upwelling water. Spatial distributions of abundance, species diversity index and assemblage structures of the larval fishes might be influenced by the upwelling which occurred alone the margins of the continental shelf.