The stable carbon (δ13C) and nitrogen (δ15N) isotope values of soft tissues of micronekton (crustaceans, squid, mesopelagic fish) and zooplankton were measured from organisms collected on the RV Antea at two seamounts located in the south-western Indian Ocean: La Pérouse (summit depth ∼60 m) and “MAD-Ridge” (thus named in this study; summit depth ∼240 m). Surface particulate organic matter (POM-Surf) showed higher δ13C at the more productive MAD-Ridge than at the oligotrophic La Pérouse seamount. Particulate organic matter and zooplankton were depleted in 15N at La Pérouse pinnacle compared with MAD-Ridge. Gelatinous organisms and crustaceans occupied the lowest and intermediate trophic levels (TL ∼2 and 3 respectively) at both seamounts. Mesopelagic fish and smaller-sized squid sampled at both seamounts occupied TL ∼3 to 4, whereas the large nektonic squid, Ommastrephes bartramii, collected at MAD-Ridge only, exhibited a TL of ∼5. The δ15N values of common open-water mesopelagic taxa were strongly influenced by specimen size and feeding habits at both seamounts, with an increase in δ15N values with increasing size. Carnivorous fish species sampled exclusively over the seamounts’ flanks and summits exhibited TL values of ∼4, irrespective of their wide size ranges. The work could not demonstrate any differences in δ15N values of mesopelagic fish between the seamounts and the surrounding oceanic areas. The study segregated clusters of mesopelagic organisms according to their δ13C and δ15N values, with variations in stable isotope values reflecting a complex range of processes possibly linked to productivity as well as biological and ecological traits of the species (size and feeding mode).