The harbor sediment containing high concentration of heavy metals may pose serious impacts on the marine ecosystem and environmental quality. The bioleaching process has been considered as an environmentally friendly and cost-effective alternative for removing heavy metals from contaminated sediments. In this study, a series of experiments were performed to investigate the feasibility of bioleaching process for removing heavy metals from the contaminated harbor sediments. The performance of the bioleaching process inoculated with sulfur-oxidizing microflora acclimated from the native harbor sediment was compared with that acclimated from the exogenous soil. In the bioleaching experiment with inoculants from native sediment, the efficiency of Zn, Cu, Cr, Pb, and Ni (30 days) reached 39-100%, 21-94%, 8-63%, 5-74%, and 19-77%, respectively. While 59-100% of Zn, 22-100% of Cu, 0-95% of Cr, 0-100% of Pb, and 22-100% of Ni were respectively removed in the bioleaching experiment with inoculants from exogenous soil after 30 days of reaction time. The results show that the rate and efficiency of metal removal in the bioleaching process decreased with an increase of sediment solid content from 10 to 40 g/L. The efficiency of metal removal in the bioleaching process with inoculants from the native sediment was lower than those from the exogenous soil due to the bacterial activity. By the fractionation of metal in the harbor sediment, exchangeable, carbonate-bound, and Fe/Mn oxide-bound metals (mobile fractions) were found to be apparently reduced and even organic matter/sulfide-bound and residual metals (stable fractions) were slightly removed after the bioleaching experiment.