Sampling campaigns were conducted onboard of R/V Bat-Galim in the course of three oceanographic cruises conducted during 2017-2019, as part of the national deep-water monitoring program of the Israeli Mediterranean Sea performed by Israel Oceanographic and Limnological Research (IOLR). Deep sea fish and crustaceans were collected by a semi-balloon trawl net in the following transects (32.588583°N 34.763598°E to 32.526467°N 34.7362113°E; 32.627207°N 34.737953°E to 32.579127°N 34.699993°E; 32.6978475°N 34.53706267°E to 32.635671°N 34.5038796°E; 32.7248886°N 34.3501125°E to 32.77411°N 34.380888°E). Sampling sites were divided into three major benthic habitats: (1) the end of the continental shelf, with an average depth of 200 m; (2) the continental slope with a depth range of 500-600 m; and (3) the deep bathyal plateau (continental rise) with a depth range of 1000-1400 m. Fourteen species of bathypelagic fishes and six species of bathybenthic decapod crustaceans were collected, weighed and their total length was measured. Bulk δ13C and δ15N isotope data of the fish and crustaceans were analyzed. Raw data include individual weight and length, δ13C, δ15N, and C/N ratio.