The aim of this study was to investigate the distribution patterns of demersal fishes on the continental shelves of the north-eastern Levantine and north-eastern Aegean seas. Fish samples were collected by bottom trawl. A total of 29 hauls were carried out, 15 hauls between 43 to 121 m depth in the north-eastern Levantine Sea and 14 hauls between 65 to 100 m depth in the north-eastern Aegean Sea. The total trawled area for both region was 1.87 km(2). Cluster analysis and non-metric multidimensional scaling were applied to identify hauls grouping. Among 114 fish species found, 84 were recorded in the north-eastern Levantine Sea and 64 in the north-eastern Aegean Sea. Fifty species were found exclusively from the northeastern Levantine Sea, 30 species exclusively from the north-eastern Aegean Sea and 34 species were shared by the two areas. The Lessepsian migrants, Upeneus moluccensis, Equulites klunzingeri, Saurida undosquamis, and the indigenous species Pagellus erythrinus were the most common species of fish assemblage in the north-eastern Levantine Sea. The most common species in the north-eastern Aegean Sea were Serranus hepatus, Mullus barbatus, Citharus linguatula, Merluccius merluecius and Lepidotrigla cavillone. Faunal composition in the north-eastern Levantine Sea was influenced by the oligotrophic, temperate and high saline water, while in the north-eastern Aegean Sea it was mainly affected by the outflow of cold, less saline and highly productive waters from the Black Sea