Trophic relationships significantly influence ecosystem functioning, ultimately affecting populations’ abundance, size structure and distribution. There is still a substantial knowledge gap on the trophic ecology of deep-sea organisms, particularly those living in the mesophotic depths (30–150 m), despite their crucial importance as ecosystem engineers. The trophic ecology of the most common mesophotic black coral species of the Mediterranean Sea, Antipathella subpinnata (Ellis & Solander, 1786), was studied by means of stable isotopes analysis in two seasons. The δ13C and δ15N analysis of the tissue of A. subpinnata, of the sediment, as well as the main planktonic fractions (pico-nanoplankton, microplankton, and mesozooplankton) indicate a diet based on pico-nanoplankton in autumn and mesozooplankton in spring. We calculated a trophic enrichment of 1‰ in δ13C and of 2.5‰ δ15N between prey and predator. Such information contributes towards drawing a complete picture of the pelagic-benthic coupling in the Mediterranean mesophotic coral forests.