Food web structure of deep-sea megafauna in the Balearic Basin (NW Mediterranean) was investigated using carbon and nitrogen stable isotopes. A total of 71 species (including 26 fish species and 19 decapod species) were analysed from samples collected with a semi-balloon otter-trawl in 2 contrasting oceanographic settings: The Catalonian Slope (CS), a continental slope area indented by several submarine canyons and an insular slope area north of Mallorca (the Balearic Slope, BS). Three faunally distinct depth zones were sampled in each area in July 2010: 450 to 600 m (upper slope), 1000 to 1300 m (middle slope) and 1400 to 2200 m (lower slope). Different physical- chemical variables and potential food sources were analysed as possible explanatory variables of trophic web variability. A δ15N- δ13C scatterplot indicated a complex food web with fish (i.e. Macrouridae and deep-sea sharks) occupying the highest trophic position. Significant differences occurred in the isotopic composition of species among upper, middle and lower slope assemblages and between the areas (CS vs. BS). Generally, higher δ15N and δ13C values were observed with increasing depth (especially among benthic feeders), and on the CS compared with the BS. Similarly, based on generalized linear models, different environmental-trophic variables ex plained the observed trends. On the BS, δ13C of species was mainly linked to physical variables and to chlorophyll a concentration at 5 m above the bottom as a proxy of marine snow, suggesting assemblages were mainly linked to vertical inputs. Conversely, on the CS, δ13C was related to trophic variables, indicating that species are linked to prey availability and less directly to primary production. The comparison suggests longer food webs over the mainland slope. © Inter-Research 2013.