Pelagic sharks are vulnerable to overfishing due to slow growth rates, late-at-maturity and low fecundity, 90% of which are Near Threatened with an elevated risk of extinction according to IUCN Red List Criteria. Trace elements can be accumulated by marine predators and may have detrimental effects on population dynamics. In this study, we analyzed the concentrations of 11 trace elements (Zn, Cu, Cr, Ni, Mn, Se, Co, Hg, Cd, Pb, and As) in muscle and liver tissues of 10 pregnant pelagic thresher sharks (Alopias pelagicus) and their 18 embryos. The results showed that four essential elements (Cu, Cr, Mn, and Se) were accumulated in both tissue types of embryos. Ni and Zn concentrations were higher in embryonic muscle than that in the liver. For nonessential elements, concentrations of As, Cd and Hg in both embryonic tissues were lower than those of their mothers. Though maternal and embryonic tissues had high levels of Hg, the Se/Hg molar ratios in both tissues of the embryo were above 1 with larger values in the embryos, indicating that Se played a protective role against Hg toxicity in embryonic tissues. Liver is the primary energy resource of embryo development. There was no correlation for element concentrations between embryonic and maternal liver tissues, indicating there is a regulatory mechanism to maintain the stability of element contents during maternal transfer in pelagic thresher shark.