Comparing larval fish assemblages in different estuaries provides insights about the coastal distribution of larval populations, larval transport, and adult spawning locations. We simultaneously compared the larval fish assemblages entering 2 Middle Atlantic Bight (MAB) estuaries (Delaware Bay and Chesapeake Bay, USA) through weekly sampling from 2007 to 2009. In total, 43 taxa (32 families) and 36 taxa (24 families) were collected in Delaware and Chesapeake Bays, respectively. Mean taxonomic diversity, mean richness, and evenness were generally lower in Delaware Bay. Communities of both bays were dominated by Anchoa spp., Gobiosoma spp., Micropogonias undulatus, and Brevoortia tyrannus; Paralichthys spp. was more abundant in Delaware Bay and Microgobius thalassinus was more abundant in Chesapeake Bay. Inter-annual variation in the larval fish communities was low at both sites, with a relatively consistent composition across years, but strong seasonal (intra-annual) variation in species composition occurred in both bays. Two groups were identified in Chesapeake Bay: a 'winter' group dominated by shelfspawned species and a 'summer' group comprising obligate estuarine species and coastal species. In Delaware Bay, 4 groups were identified: a 'summer' group of mainly obligate estuarine fishes being replaced by a 'fall' group; 'winter' and 'spring' groups were dominated by shelf-spawned and obligate estuarine species, respectively. This study demonstrates that inexpensive and simultaneous sampling in different estuaries provides important insights into the variability in community structure of fish assemblages at large spatial scales.KEY WORDS: Estuarine systems · Young-of-the-year · Community composition · Temporal variability · Ichthyoplankton · Middle Atlantic Bight Resale or republication not permitted without written consent of the publisher