The present work on mesozooplankton of the Ionian Sea is part of a study aimed at assessing if the epipelagic communities had been affected by the changes in circulation (named EMT, Eastern Mediterranean Transient) observed in the eastern Mediterranean starting from 1988 as a transient effect of climate forcing. A temporal comparison was performed on data obtained in the springs of 1999 and 1992, periods characterized by opposite patterns in the upper circulation that in 1998 reversed from an anticyclonic to a cyclonic flow. A spatial comparison was performed on the data collected in 1999 from areas that previous oceanographic surveys had shown to be diversely affected by the EMT. Interannual differences were observed in the distribution of mesozooplankton abundance in the upper layer that might be related to the EMT dynamics and the effects of the reversed circulation. In 1999, abundance and composition of epipelagic mesozooplankton differed between the northwestern and eastern areas of the Ionian Sea. The distribution of species, trophic groups and copepod gut pigments suggested that different pelagic food webs took place at the opposite sides of the basin. A classic type food web prevailed in the northwestern, more productive area, whereas the microbial links prevailed in the eastern, more oligotrophic area. The characteristics of the northwestern area may in large part be due to the enrichment effects of the cyclonic circulation enhanced by the nutricline uprise due to the EMT, and to the interaction between the cyclonic circulation and the continental slope.