This study aimed to develop a simpler method for determining total mercury (T-Hg) and methylmercury (MeHg) in biological samples by using methyl isobutyl ketone (MIBK) in the degreasing step. The fat in the samples was extracted by MIBK to the upper phase. T-Hg transferred into the water phase. This was followed by the extraction of MeHg from the water phase using HBr, CuCl2 and toluene. The MeHg fraction was reverse-extracted into L-cysteine-sodium acetate solution from toluene. The concentrations of T-Hg and MeHg were determined by heating vaporization atomic absorption spectrometry. Certified reference materials for T-Hg and MeHg in hair and fish were accurately measured using this method. This method was then applied to determine T-Hg and MeHg concentrations in the muscle, liver and gonads of seafood for the risk assessment of MeHg exposure. The mean T-Hg and MeHg concentrations in squid eggs were 0.023 and 0.022 µg/g, and in squid nidamental glands 0.052 and 0.049 µg/g, respectively. The MeHg/T-Hg ratios in the eggs and nidamental glands of squid were 94.4% and 96.5%, respectively. The mean T-Hg and MeHg concentrations in the gonads of sea urchins were 0.043 and 0.001 µg/g, respectively, with a MeHg/T-Hg ratio of 3.5%. We developed an efficient analytical method for T-Hg and MeHg using MIBK in the degreasing step. The new information on MeHg concentration and MeHg/T-Hg ratios in the egg or nidamental glands of squid and gonads of sea urchin will also be useful for risk assessment of mercury in seafood.