Halogenated organic compounds having many beneficial applications, both in industries and agriculture sectors. Basically, the uses are as pesticides, solvents, surfactants, and plastics. However, their large, widespread uses throughout the world have resulted the negative impact on the environment. Considering their treatment process are widely accepted by using the bioreactor systems. The large variety of microorganisms present in the bioreactor and their interaction is the key to the effective treatment and removal of these compounds. Usually the microbes produce the enzymes known as dehalogenase to remove the halogen form the compounds to make it non-toxic. Many of the different steps and about the microbial groups in degradation process of halogenated compounds are well understood, but more details concerning the microbial community are yet to be discovered. This chapter describes about the different dehalogenation systems available in microbes and their ultimate application in different bioreactor systems for the degradation analysis of several harmful halogenated compounds.