Submarine canyons act as hotspots of biodiversity, hosting vulnerable marine ecosystems, and playing a fundamental role in bridging coastal zones with deeper areas. Here, we investigated the suprabenthic and Deep Scattering Layer (DSL) zooplankton fauna, that play a key role in deep-sea food webs, as main resources for both mobile and sessile megafauna, in two submarine canyons (Squillace and Amendolara) of the Ionian Sea (Central Mediterranean Sea). Our results highlighted different taxonomic and functional diversity between the two adjacent canyons: i) biomass and abundance of suprabenthos followed an opposite trend in the two canyons, increasing both with depth in Amendolara (higher abundance and biomass in the lower part of the canyon), and decreasing with depth in Squillace (greater in the head of the canyon); ii) DSL zooplankton abundance and biomass followed a spatial distribution, decreasing with increasing distance from the coast for both canyons (i.e. lower offshore than at the head of the canyon). Food-web structure investigated by means of stable isotope analysis of δ13C and δ15N showed a more diverse trophic niche for suprabenthos than for zooplankton. Furthermore, possible feeding modes of species with unknown feeding behaviour have been proposed. The results of the current article highlight the different ecological processes occurring within each canyon. Understanding the spatial variations of communities inhabiting submarine canyons, especially those at the base of deep-sea food webs which can act as driver of megafaunal communities (both sessile and mobile-commercial species), is essential to focalise future conservation efforts.