<p>Mercury (Hg) biomagnification in food webs is crucial for understanding ecological risks of Hg exposure and has become a pressing global concern. Recent research suggests that Hg biomagnification is a complex biological and ecological process. For instance, Hg readily binds to the amino acid cysteine, forming Hg-cysteine complexes that may play a key role in bioaccumulation. However, evidence of Hg transfer through oceanic food web remains limited, and the role of Hg-cysteine complexes has yet to be systematically explored or compared across oceanic species. Here, we employed an integrated approach utilizing total mercury (THg), methylmercury (MeHg), stable carbon and nitrogen isotopes, and amino acid concentrations to investigate Hg biomagnification mechanisms in 16 epipelagic and mesopelagic organisms (116 samples) from the tropical western Pacific, including crustacean zooplankton, cephalopods, teleost fish and sharks. The results of stable isotope analysis showed interspecific trophic positions ranging from 2.00 to 4.32. A significant positive linear relationship was found between the natural logarithm of THg or MeHg concentrations (μg·g⁻¹ dw) and trophic positions. The trophic magnification factor values all exceeded 1, indicating clear biomagnification across successive trophic positions. In addition, a positive relationship between logarithm of cysteine and THg or MeHg (excluding shark species) suggests that Hg-cysteine complexes may play a key role in Hg bioaccumulation in teleost. However, this mechanism may not apply for elasmobranchs. Our findings demonstrate a high rate of Hg biomagnification in the tropical western Pacific and highlights the potential role of cysteine in modulating Hg transfer. These insights can improve ecological risk assessment of Hg in oceanic ecosystems and enhance our understanding of Hg trophic dynamics at the molecular level.</p> Graphical abstract <p></p>