From August 2009 to August 2010, larval and juvenile fishes were monthly collected by a seine net(1m×4m，1 mm meshaperture) in the surf zones of south branch of Yangtze River estuary and north coast of Hangzhou Bay. 267 hauls were conducted in the Yangtze River estuary, and a total of 11 066 catches belonging to 43 species from 23 families were collected, the most dominant species was Coilia nasus which comprised 64.44% of the total catches.195 hauls were conducted in Hangzhou Bay, a total of 3 841 catches belonging to 62 species from 23 families were collected, Acentrogobius pflaumii and Eleutheronema rhadinum comprised 61.73% of the total catches. The differences of geography and aquatic environment between two areas affected composition of fish assemblage, while 26 mutual species occurred, the dissimilarity index still rose to 0.927. Developmental stage of fish larvae and juveniles also showed some differences, postflexion and juvenile fish dominated the total catches in Hangzhou Bay, whereas the variation in Yangtze River estuary was not in evidence.Community diversity of Hangzhou Bay is higher than that of the Yangtze River estuary, and the Margalef index, ShannonWierner index and Pielou eveness index were all higher. Kdominance curves revealed that the species richness was higher in Hangzhou Bay.