This study presents the results obtained from a DNA barcoding survey of the deep-sea macro- and mega-fauna off the Israeli coast (SE Mediterranean, depths of 700 to 1500 meters; during the years 2012-2013). Using trawling and gilhietting we collected 846 organisms, assigned to 37 species, consisting of fish (18). crustaceans (10). mollusks (5), echinoderms (3) and a single brachiopod. The most abundant species were the blackinouth catshark Galeus melastomus, the cosmopolitan decapod Polycheles typhlops and the bivalve Abra longicallus. Two species were sampled for the first time in the southern Levant: the long anned chiroteuthid squid, Chiroteuthis veranyi, and the common mora, Mora moro. Four of the 18 fish species represented 78% of the total fish collected, and two of the 10 crustacean species represented 61% of the total crustaceans collected were abundant. Most other species were represented by fewer than 10 individuals. PCR products for the cytochrome c oxidase sub unit 1(COI) gene were successfully sequenced for the 37 species (1-3 vouchers/species). The vouchered individuals were stored at the Steinhardt Museum of Natural History (Tel Aviv University, Israel) and their COI sequences were uploaded to the BOLD universal data center as part of the Israeli national marine barcoding project. The COI sequences of Acantlzephyra eximia, Gryphus vitreus, Galeodea echinophora, Mesothuria intestinalis and Astropecten irregukuis, are the first records of these species in the BoLD. When compared to the COI sequences in BoLD, the present results reveal some inconsistencies in species identification. This outcome should be taken into consideration, calling for further meticulous taxonomical work on some BoLD vouchered specimens. This study is the first step in the DNA barcoding of the little-known Levant's benthic deep-sea fauna.