Mercury and selenium were measured for first time in the endangered species whale shark (Rhyncodon typus) from two areas of the Gulf of California, Bahía Los Angeles (BLA) and Bahía La Paz (LAP) using dermal biopsies of seventy specimens. Additionally, nineteen zooplankton samples from LAP were analysed. Concentrations (ng/g, wet weight (ww)) in biopsies of BLA ranged from 1 to 40 for Hg and 100 to 680 for Se; while in LAP varied from 1 to 9 for Hg and 11 to 850 for Se. A positive correlation was found for Hg in BLA males biopsies with length. Hg and Se concentrations in the zooplankton from LAP were 1.6 ± 1.8 and 770 ± 930 ng/g, respectively. Hg biomagnification factor ranged from 0.8 to 5.3 in sharks. A molar excess of Se over Hg was found in the biopsies and the zooplankton.