Trace elements and δ15N values were analysed in micronekton (crustaceans, fishes and squids) sampled in the south-western Indian Ocean. Myctophids were associated with high concentrations of arsenic at La Pérouse and MAD-Ridge seamounts, and with lead and manganese at MAD-Ridge and in the Mozambique Channel. The difference in cadmium, copper and zinc concentrations between micronekton broad categories reflected differing metabolic and storage processes. When significant, negative relationships were found between micronekton body size and trace element concentrations, which can possibly be attributed to differing metabolic activity in young and old individuals, dietary shifts and/or dilution effect of growth. No relationships were found between trace element concentrations and δ15N values of micronekton (except cobalt which decreased with increasing δ15N values), since most trace elements are not biomagnified in food webs due to regulation and excretion processes within organisms. All trace element pairs were positively correlated in fishes suggesting regulation processes.