Seagrass are globally known as an essential habitat for marine fishes. The study of fish assemblages in seagrass ecosystem is needed as the first base to select the most suitable coastal fisheries management. The study aims to reveal the composition of fish assemblages both seasonally and spatially in Karang Congkak Island, Kepulauan Seribu. Sampling was performed six times in NW monsoon (March), first transitional monsoon (April-May) and SE monsoon (Juni, August, September) 2018. Fish were sampled at four sites at seagrass ecosystem of Karang Congkak Island, namely eastern, southern, western, and northern by using beach seine net. The differences of juvenile fish assemblages were analyzed using One-Way ANOSIM. A total of 6,326 fish were collected belonging to 78 species, 31 families and 10 orders in which Labridae was the most diverse family. The result indicates strong spatial and temporal variation in fish composition. Fish compositions were dominated by juvenile both spatially and temporally. The most common species that inhabits seagrass beds of the Karang Congkak Island as temporary resident such as Gerres oyena and Siganus canaliculatus, and regular visitor namely Halichoeres argus. Cannonical correspondence analysis indicated strong correlation between several fish species and environmental variables.