Natural abundance values of stable isotopes (δ13C and δ15N) were measured in three pooled size-based groups of zooplankton (50–200, 200–500, and >500 µm) and 78 species or genera from the hyperbenthic and pelagic domains. The taxonomic records include 23 decapod crustaceans, 21 cephalopods, 1 gastropod, 17 osteichthyes, 2 chondrichthyes, 7 peracarids, 1 echinoderm, 2 thaliaceans and 1 brachyopod. This dataset comprises 815 records, including δ13C, δ15N, %C and %N, which were obtained, depending on the species size, from bulk tissues, whole or pooled individuals. It also provides the count and size (in mm) of sampled organisms from the dominant species in the area, representing 70% of the total catch in terms of total biomass or numerical abundance (Quetglas et al. 2014; Olivar et al. 2012; Simao et al. 2014). Sampling was conducted off southern (Cabrera) and northwestern (Sóller) Mallorca (Balearic Islands, western Mediterranean) at three depths (Massutí et al. 2014): continental shelf break (250 m), upper slope (650 m) and middle slope (850 m). Two surveys were performed: the first in December 2009 (late autumn) and the second in July 2010 (summer). Through stable isotope based techniques, this dataset was used to explore production sources, trophic structure and benthic-pelagic coupling in two geographically close but hydrographically contrasting areas: Sóller vs. Cabrera (Valls et al. 2014a, 2014b).Samples were collected with both pelagic and benthic sampling methods, performed simultaneously from two vessels: (1) a commercial fishing boat to sample the nektobenthic, suprabenthic and epibenthic communities; and (2) an oceanographic vessel to sample the pelagic communities. Benthic sampling was carried out using three gear types: (i) a commercial bottom trawl gear with a 20 mm diamond mesh cod-end (huelvano-type) to collect nekto-benthic species (Rueda et al., 2014); (ii) a beam trawl (10 mm diamond mesh cod-end) for sampling the epifauna (Ramon et al. 2014); and (iii) rectangular net rigged in the beam-trawl to catch suprabenthic fauna within 0.6 m above the bottom (Herrera et al. 2014).Mesopelagic fauna was sampled with a mid-water trawl (10-mm diamond mesh cod-end (Olivar et al. 2012). Zooplankton samples were collected by vertical hauls in the 0–200 m water column at two bathymetric strata (200 and 900 m) within each study area. A double Calvet net (53 μm mesh size) was used to collect microzooplankton and a triple WP2 net (200 μm mesh size) was used for the collection of meso- and macrozooplankton (Puelles et al. 2014). Additionally, particulate organic matter (POM) was collected one-year-round using sediment traps moored at 800 m depth (30 m above the bottom); corresponding POC and PON isotopic values are available in Pasqual et al. (2015). More details on zooplankton and demersal species sampling can be found in Massutí et al. (2014). All the stable isotopic analyses were performed using a Thermo DELTA X-PLUS mass spectrometer at the Scientific-Technical Services of the University of the Balearic Islands.