Species-specific isotope dilution inductively coupled plasma quadrupole mass spectrometry reference method and high-performance liquid chromatography were applied for simultaneous determination of mercury species in marine samples. Different extraction protocols for mercury species were tested and evaluated. It was found that after exposure to microwave energy the inorganic mercury (iHg) and methyl mercury (MeHg) can be completely extracted from marine biota sample by 4.5 mol L−1 HCl as well as by 3.0 mol L−1 HNO3 and further separated with HPLC. The obtained results for iHg and MeHg in the IAEA-461 certified reference material (CRM) clam Gafrarium tumidum biota sample were as follow: (341 ± 21) μg kg−1 or (338 ± 15) μg kg−1 and (61.3 ± 2.2) μg kg−1 (recovery of (98.4 ± 3.6) %) or (61.1 ± 2.8) μg kg−1 (recovery of (98.1 ± 4.6) %), respectively when diluted HCl or HNO3 were applied in the extraction step. However, these protocols are not applicable to marine sediment samples, where the iHg is the predominant form. Therefore, one selective extraction procedure for MeHg from sediment was applied to make possible its separation and quantification. This procedure consisted of series of subsequent extraction steps at room temperature: first with a mixture of H2SO4/KBr/CuSO4, next with organic solvent dichloromethane and as a final step one back-extraction with Na2S2O3 solution. The combination of the selective extraction with the ID calibration approach was found to be an efficient way for the simultaneous determination and separation of both MeHg and iHg species in one chromatographic run. The proposed procedure was successfully used for the determination of mercury species in the IAEA-405 sediment CRM and further applied for the simultaneous measurements of iHg and MeHg in a candidate CRM – the IAEA-475 sediment sample. The determined mass fractions were (30.1 ± 1.6) μg kg−1 and (196 ± 8) ng kg−1 for iHg and MeHg, respectively. The difference between obtained in this study results and those from the reference IAEA-475 values was 1.5% and further validated the developed in this study analytical methodology. To the best of our knowledge, this selective procedure for MeHg extraction was never used before for the simultaneous quantification of mercury species in marine sediment.