The combination of HPLC, oxidative decomposition by UV irradiation, and cold vapor atomic fluorescence spectrometry (HPLC-UV-CVAFS) was applied to the fractional determination of mercury species, which were contained in biological samples, such as seafood. Firstly, the extraction of mercury species from biological samples was studied, and it was found that 2-mercaptoethanol (2-ME), which has a mercapto group, was an effective extractant. For three certified reference materials, which have the certified values of the CH3Hg+ concentration, extraction by a 2-ME solution and the HPLC-UV-CVAFS measurement were carried out. It was confirmed that the measured values were about the same as the certified values. The same analytical method was applied to real seafood samples. The sum of the CH3Hg+ concentration and the Hg2+ concentration in the extraction solution, which was obtained by the HPLC-UV-CVAFS measurement, was about the same as the total mercury concentration obtained by the heat vaporization atomic absorption spectrometry (HVAAS) measurement. Therefore, it is evident that the fractional determination of mercury species in biological samples was favorably performed when the extraction solution obtained by the 2-ME extraction was analyzed by HPLC-UV-CVAFS.