The distribution of methylmercury (MeHg) and total mercury (T-Hg) in sediments of the estuaries and the basin in Kaohsiung Harbor (Taiwan) is studied. MeHg in the sediment samples was determined using gas chromatography-mass spectrometry. The certified reference material of sediments with respect to the method showed the recovery efficiency between 97.4 and 103.6% which confirmed the applicability of analysis method. The T-Hg and MeHg concentrations were between 149 to 9035 μg/kg and <0.31 to 17.7 μg/kg, respectively. The T-Hg and MeHg concentrations in the estuaries of Kaohsiung Harbor were relatively high. Results suggest that Hg in this studied area was likely contributed from the catchments of the rivers. The MeHg level was <0.01 to 2.66% of the T-Hg in the sediments. A positive correlation is obtained between MeHg, T-Hg, and total organic carbon in the sediments, whereas a negative correlation is observed between pH, oxidation-reduction potential, and MeHg concentration. The results further suggest that sediment characteristics contribute mainly to the distribution of MeHg.