Patterns in the mesoscale distribution of larval fish in the coastal waters of central Greece, an area of high topographic and bathymetric complexity, were analysed using samples collected during two ichthyoplankton surveys in July 1998 and June 1999. Salinities were lower in the eastern (Aegean) part of the study area due to the influence of waters originating from the Black Sea. In this region, larvae of many epipelagic and benthopelagic (typically summer spawning) species were less abundant in June 1999, when waters were significantly cooler, compared to July 1998. Multivariate analyses identified ‘neritic’ and ‘pelagic’ groups of stations dominated by larvae of epipelagic/bethopelagic (typically shelf dwelling) and mesopelagic species. In the west (Ionian Sea), a prominent third group of stations located in the deep and highly enclosed Korinthiakos Gulf was also defined with very high abundances of mesopelagic fish larvae. However, the genera Cyclothone and Vinciguerria that dominated the neighbouring offshore assemblage of the Ionian Sea were absent from this gulf. In the study area, Korinthiakós Gulf (>900 m) and North Evoikos (>400 m) Gulf comprise unique ‘fjord-like’ ecosystems in the Mediterranean with increased productivity and significantly cooler deep waters compared to adjacent open sea basins.