In this study, based on the data acquired in seasonal comprehensive surveys of the marine ecosystem of the Jiulong River Estuary from Sep.2010 to Aug.2011, the composition, quantity distribution and variation of fish species were reported with relative species number and weight. The results showed: a total of 169 fish species were collected in this survey, which belonged to 18 orders, 63 families and 118 genera. 89 fishes from the family Perciformes(accounting for 52.7% of the total species), 18 fishes from the family Cypriniformes and 16 from Clupeiformes respectively(10.7％ and 9.5％of the total species respectively). And there were 59.8% warm water fishes, 37.8% warm temperature fishes and 2.3% cold temperature fishes. And a total of 98 fish species were collected in Daomei site; a total of 96 fish species in Fugong site；a total of 87 fish species in Zini site. Shannon Weaver biodiversity index H was higher in Daomei site and lower in Fugong site，and the average biodiversity index of fish were 2.816 8 and 2.060 4 respectively. 〖WTBX〗Anchoviell ach inensis,Ambassis gymnocephalus〖WTBZ〗 and 〖WTBX〗Mudil affinis 〖WTBZ〗Günther were the dominant fishs in Jiulong River Estuary, whose annual frequency exceeded 50% separately. The abundance of fishery resource was high in autumn（from Sep. to Nov.）,followed by summer ,and the lowest in winter（from Dec. to Feb.）.Annual fish assemblage characteristics are closely related to estuary runoff. And during the flood season, the fish concentration of Fugong (confluence of seawater and freshwater) showed characteristics closer to that of Zini (freshwater area); but in other times, the fish concentration of Fugong(confluence of seawater and freshwater) showed characteristics closer to that of Daomei(the salt water area).