The elucidation of the catalytic role of LinA dehydrohalogenase in the degradation processes of hexachlorocyclohexane (HCH) isomers is extremely important to further studies on the bioremediation of HCH polluted areas. Herein, QM/MM free energy simulations are employed to provide the details of the dehydro chlorination reaction of two HCH isomers (gamma and beta). In particular, the role of the protonation state of one of the catalytic residues-His73-is explored. Based on our calculations, two distinct minimum free energy pathways (concerted and stepwise) were found for gamma-HCH and beta-HCH. The choice of the reaction channel for the dehydrochlorination reactions of gamma- and beta-HCH was shown to depend on the initial mutual orientations of the reacting species in the active site and the protonation form of His73. The sequential pathway comprises the transfer of the proton (H-delta 1) between His73 and Asp2S and subsequently the H-1/Cl-2 pair elimination from the substrate molecule. Within a concerted mechanism, the dehydrochlorination reaction of gamma-/beta-HCH is initiated with neutral His73 and the H-delta 1 proton is transferred upon final product formation. We found that the concerted pathway for beta-HCH results in significantly higher free energy of activation than the stepwise route and therefore can be disregarded as not a feasible mechanism. On the other hand, the reaction that occurs with much lower energetic barrier requires a stronger base (i.e., anionic His73) to abstract the proton (H-1) from the substrate molecule. The presence of such transient form of His results in higher energy than the respective Michaelis complex and was observed only in the stepwise pathway for both isomers. Furthermore, we have concluded that both pathways (concerted and stepwise) are feasible for the dehydrochlorination reaction of gamma-HCH. The activation free energies obtained from the M05-2X/6-31+G(d,p) corrected path coordinate PMF profiles for the dehydrochlorination reactions of the gamma-/beta-HCH are in good agreement with the experimental values.