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Monitoring the impacts of global efforts to reduce mercury (Hg) emissions is limited by the collection of biological samples at appropriate spatiotemporal scales. This is especially true in the deep sea, a vast region with food webs that cycle bioaccumulative methylmercury (MeHg). Within a species, understanding the distribution of Hg across tissue types can reveal how Hg accumulates in the body and inform how useful a species is for biomonitoring geographic regions or vertical habitats of the ocean. We focus on a globally distributed deep-sea fish, the longnose lancetfish (Alepisaurus ferox, n = 69 individuals), and measure total mercury (THg) and MeHg concentrations in 10 tissue types (brain, caudal white muscle, dorsal white muscle, gallbladder, gill filament, gonad, heart, intestine, liver, and stomach lining). Across all tissue types, THg and MeHg concentrations were higher in large lancetfish (≥1.8 kg) than small lancetfish (<1.8 kg), but concentrations were relatively stable within size classes. THg levels were highest in liver, intestine, and heart, followed by caudal white muscle, dorsal white muscle, stomach lining, and gill filament, then by gonad and gallbladder. We describe how ontogenetic diet shifts explain Hg bioaccumulation in pelagic predators inhabiting similar waters to lancetfish. We hypothesize that diet shifts to deeper-dwelling prey and fishes drive increases in THg and MeHg concentrations in large lancetfish. We propose lancetfish as a strong candidate for monitoring spatiotemporal variability of Hg in the deep pelagic – they are commonly captured in global fisheries and may reflect Hg sources in two distinct vertical habitats of the ocean.