Mesozooplankton samples were collected within the project Physical Oceanography of Easten Mediterranean-Biology-Chemistry (POEM-BC). Samples were collected on board of R/V AEGAIO from 92/3/20 till 92/4/15 in the NW Levantine Sea (34.5 N   23 till 36.5N  28.5E) and in the  S.Aegean Sea (36N 24E till 36N 27E). Samples were collected at discrete layers (from the surface till 300m) by vertical tows of a WP-2 net (200 μm) and their taxonomic analysis was performed by Binocular microscope in the laboratory of zooplankton-Institute of Oceanography-Hellenic Centre for Marine research. The data set concerns Taxon-specific mesozooplankton abundance and total mesozooplankton abundance. The dataset includes 55 samples with data of mesozooplankton species composition and abundance. These data are partially published.