The trophic structure of deep-sea fish communities has been poorly studied in the Southeastern Pacific Ocean. Here, using the analysis of multiple (CNS) stable isotopes, we provide a first approach to characterize the structure of a marine food web including mesopelagic (9 species) and demersal (13 species) fishes. At a species level, Dissostichus eleginoides were the most 13C-depleted and the grenadier Coryphaenoides ariommus the most 13C-enriched species. The most 15N-depleted species was the lanternfish Diogenichthys laternatus and macrourid fishes Trachyrincus villagai and C. ariommus the most 15N-enriched. δ34S values showed less variation, but ranged considerably, varying between 10.5 and 17.7‰: C. ariommus was the most 34S-depleted species and D. eleginoides the most 34S-enriched. At a whole study level, individual δ13C and δ15N values were positively correlated. Relationships between δ13C and δ34S, and δ15N and δ34S were both negative. When analyses were conducted separately for demersal and mesopelagic fishes, δ13C showed a positive correlation with δ15N. There was a negative relationship between δ13C and δ34S in demersal fish but no apparent relationship between δ15N and δ34S. In mesopelagic fishes, there was no statistical support for relationships between δ13C and δ34S or δ15N and δ34S. Mean log-transformed total length (TL) and mean δ15N were related in mesopelagic fishes, but there was no apparent relationship between TL and δ13C or δ34S values. In the case of demersal fishes there was no relationship between TL and either δ15N, δ13C or δ34S. Using cluster analysis, species were classified into 4 distinct trophic groups (G1 - G4) that display different trophic strategies according to the literature. Groups G1 and G2 included zooplanktivorous, micronektonivorous and gelatinovorous fishes associated with pelagic habitats. Groups G3 and G4 include micronektonivorous, piscivorous and generalist fishes foraging in benthic habitats. The demersal fish Dissostichus eleginoides was classified as a member of G1, suggesting that its diet in northern Chile is likely dominated by pelagic prey. In addition, Macrourus holotrachys (G3) showed very marked individual variability in δ15N values indicating considerable intraspecific variation in diet and foraging behavior. Given that this species had isotope values that extended across values typical of benthic and pelagic habitats, it suggests that some individuals may perform vertical migrations. Our results also highlighted that some demersal species (M. holotrachys and Coryphaenoides ariommus) had δ34S values that indicate the assimilation of some chemosynthetic-derived sulfur.Our results provide isotopic information on deep-water species in this region and show likely coupling between the demersal and mesopelagic assemblages. This information improves our understanding of deep-sea ecosystem functioning and provides key information for fisheries management and conservation initiatives.