Mercury (Hg) pollution is a global problem affecting remote areas of the open ocean, but the bioaccumulation of this neurotoxic pollutant in tropical top predators remains poorly documented. The objective of this study was to determine Hg contamination of the seabird community nesting on Clipperton Island using blood and feathers to investigate short and longer-term contamination, respectively. We examined the significance of various factors (species, sex, feeding habitat [δ13C] and trophic position [δ15N]) on Hg concentrations in six seabird species. Among species, Great Frigatebirds had the highest Hg concentrations in blood and feathers, boobies had intermediate values, and Brown Noddies and Sooty Terns the lowest. At the interspecific level, although δ13C values segregated boobies from frigatebirds and noddies/terns, Hg concentrations were explained by neither δ13C nor δ15N values. At the intraspecific level, both Hg concentrations in blood and feathers show relatively small variations (16–32 and 26–74%, respectively), suggesting that feeding ecology had low seasonal variation among individuals. Despite most species being sexually dimorphic, differences in Hg contamination according to sex was detected only in Brown Boobies during the breeding period. Indeed, female Brown Boobies feed at a higher trophic level and in a different area than males during this period, resulting in higher blood Hg concentrations. The present study also shows that most of the seabirds sampled at Clipperton Island had little or no exposure to Hg toxicity, with 30% in the no risk category and 70% in the low risk category.