The response of larval fish communities of the northeastern Aegean Sea (NEA) to interannual environmental changes is analyzed using data from four ichthyoplankton surveys covering the NEA continental shelf during June 1993, 1994, 1995, and 1996. Waters were significantly cooler, less saline and richer in zooplankton in 1993 and 1996 (‘cold’ years) than in 1994 and 1995 (‘warm’ years). A comparison of monthly SST series (1993–1997) between the NEA, the Marmara Sea, and the Western Black Sea revealed high correlations and similar trend components among these areas implying that oceanographic conditions over the NEA (and observed inter-annual differences) were most likely dominated by the properties and relative amount of Black Sea water inflow in the NEA. The relative composition of the larval fish community was significantly related to the ‘cold/warm’ regime and larval diversity was higher during the warm years. Larvae of the small-sized pelagic species, such as anchovy (Engraulis encrasicolus), and most mesopelagic fishes were relatively more abundant during the cold, zooplankton-rich years. Larvae of the middle-sized pelagics (Sardinella aurita, Scomber japonicus, Trachurus mediterraneaus, Auxis rochei) and certain benthopelagic species exhibited an opposite trend, i.e., they were more abundant during the warm years or absent during the cold years. Most of these species are known to be typical summer spawners (e.g., Serranus cabrilla, Lisa saliens, Trachinus draco, and Symphurus nigrescens). Co-variation in larval fish production might be indicative of similar responses among species to changing physical and/or trophic regimes.