Species composition, abundance and diversity of fish larvae were assessed in the Strymonikos and Ierissos Gulfs (northern Aegean Sea, Greece). Both gulfs are affected by the freshwater input of the Rivers Strymon and Rihios; water depth does not exceed 80 m. Samples were collected using a bongo net sampler (250 µm mesh size) over a grid of 35 stations in six cruises between June 1997 and May 1998. A total of 48 taxa of fish larvae (36 species, 5 genera and 7 families) were identified. The majority of identified fish larvae taxa consisted of demersal species that included larvae of Bothidae, Gobiidae, Callionymidae, Sparidae and Serranidae. The highest number of species occurred in the warm season (May, June, July, September) and this was attributed to the summer spawners that start their reproduction period during spring/early summer. The European anchovy (Engraulis encrasicolus) was the dominant species between July and September, and the European sardine (Sardina pilchardus) between November and March. Two distinct seasons (warm and cold) were identified by multivariate analysis, highlighting the importance of seasonality in shaping the community structure. The absence of well-defined larval fish associations revealed the importance of depth in the identification of different spatial patterns in an area.