Abstract The principal objectives of this research are to investigate the distribution of fish larvae in relation to environmental factors in Chiku lagoon and the coastal waters of Tainan, Southwestern Taiwan during the period from August 1998 to June 1999 and during August 13~14, 1997. Seventy-six species of the fish larvae belonging to 65 genera were identified in Chiku lagoon and the mean numerical abundance of the fish larvae was 29 ¡Ó44 inds./100m3 during the sampling period between August 1998 and June 1999; and the dominant species were Omobranchus fasciolaticeps¡BGobiidae gen. sp.¡BSillago maculata and Engraulis japonica. Seventy-two species of the fish larvae belonging to 66 genera were identified in the coastal waters off Chiku lagoon during two cruises of December 1998 and June 1999, with the mean numerical abundance of 35 ¡Ó24 inds./100m3 ; and the dominant species were Myctophidae gen. sp., Ceratoscopelus warming, S. maculata and E. japonica. Eighty-three species of fish larvae belonging to 73 genera were identified and the mean numerical abundance was 35 ¡Ó49 inds./100m3 during the cruise of August 13~14, 1997 at 6 stations along a transect from the coastal waters near Tsengwen River to the waters south of Penghu Island, and the dominant species were Bothidae gen. sp., Stomioidae gen. sp. and Mullidae gen. sp.. The abundance, species number and species diversity of fish larvae were usually higher in the coastal waters of Tainan than in Chiku lagoon. The larval fish assemblages of Chiku lagoon was significantly different from that of the coastal waters of Tainan. The dominant species of fish larvae in the coastal water of Tainan were mostly meso-epipelagic species¡]Myctophidae, C. warningi, Diaphus sp., and Carangidae¡^, while Chiku lagoon was dominated by sandy benthic species¡]Blenniidae¡^and estuarine species ¡]Gobiidae and Engraulidae¡^. The species number and abundance of fish larvae in the coastal water of Tainan were found higher in wet season¡]June¡^than in dry season¡]December¡^. The abundance of fish larvae was significantly different among stations and seasons, but did not different between tides in Chiku lagoon. The abundance of fish larvae was higher at night than during the day in August, 1998 and was usually higher in spring ¡]April¡^and lower at the middle station of Chiku lagoon. The abundance of fish larvae was not significantly correlated with water temperature and salinity, but higher abundance of fish larvae was always found when temperature was between 26¢Jand 30¢J, and in higher salinity ¡]34‰ ~36‰¡^. In the transect study, the abundance of fish larvae was significantly different between surface and deep tows¡]p<0.05¡^, but not among stations and between day and night (p>0.05).