ABSTRACT. – The spatial distribution and species richness of ichthyoplankton have been investigated using samples from two commercially important fishing areas of the North Aegean Sea (Thermaikos and Chalkidiki Gulfs, East Mediterranean Sea) in June 2004, 2005 and 2006. A total of 62 taxa were identified in this study something which is in agreement with other relevant studies of a wider spatial scale in the East and West Mediterranean Sea. The horizontal distribution of fish larvae was spatially segregated. Epipelagic, mesopelagic and demersal taxa occupied different geographical areas. Species richness and larvae abundance were significantly positively correlated with depth. Three ecological indicators, total taxa abundance, species richness and Shannon-Wiener diversity, were used to measure the diversity of the two areas. The relationship between environment and ichthyoplankton was tested with permutational multivariate analysis of variance using seven environmental factors as predictors. Topography and the physicochemical factors salinity and depth-integrated chlorophyll-a constitute the main factors affecting species richness of our study area. Analysis of similarities showed significant differences between the biocommunities in the span of the three years. The Chalkidiki area showed higher species richness and Shannon-Wiener diversity than the Thermaikos area, something, which is probably due to the different characteristics of water masses and also due to the variety of benthic habitats that Chalkidiki offers. Notably, in the Thermaikos Gulf, European anchovy and Round sardinella exhibited a strong domination pattern while mesopelagic larvae abundance and occurrence was higher at the deeper Chalkidiki area. Physicochemical parameters affected biodiversity by creating favorable conditions for adult spawning.