In this paper, an in situ bioremediation method is proposed for dioxin contaminated sediments and its efficiency is assessed in laboratory tests including microbial analysis. The main outcomes of this research are (1) Proposal of an in situ bioremediation method using anaerobic micro-organisms monitored by molecular microbial techniques. (2) It was shown that the proposed method can reduce dioxin concentrations and can increase populations of the dehalogenating micro-organism (Dehalococcoides sp.). (3) It was further shown that the dioxin degradation processes can be monitored using polymerase chain reaction (PCR) denaturing gradient gel electrophoresis and real-time PCR. Microbial analysis using molecular techniques was useful for the monitoring and management of the sediment remediation process.