Abstract: Fragmentation patterns of six polychlorinated biphenyls(PCBs) under electron impact ionization(EI) and atmospheric pressure chemical ionization(APCI) mode were compared. In the negative APCI source, there were not quasi-molecular ions and only adduct ions whose masses were 19 u less than their corresponding molecular weights existed. The intensity variation trend of these adduct ions corresponds well with those of their corresponding molecular isotopic ions detected in EI-MS mode. By using different mobile phases, it was proposed that these adduct ions may be generated by losing one chloride atom, capturing one hydroxyl from water in the mobile phase, and losing one proton. The fragmentation patterns facilitates the identification of polychlorinated biphenyls.