This study investigated the reduction of one antibiotic resistance gene (ARG, sul1) and one integron (intI1) within a multiple-antibiotic-resistant bacterium (ARB), Pseudomonas. HLS-6, during UV, chlorination and UV/chlorination. This bacterial strain was easily inactivated by these three methods, but its gene inactivation was not so easy. Two short target gene sequences (sul1-qPCR and intI1-qPCR) were selected for quantitative analysis, and another two longer ones (sul1-PCR and intI1-PCR) were used for qualitative identification. During the initial reaction time (<20 min), the degradation rate order of sul1-qPCR and intI1-qPCR was as follows: UV/chlorination>chlorination>UV. The log reduction of sul1-qPCR and intI1-qPCR in UV/chlorination achieved >3.50 and 4.00 log, respectively. The removal efficiency of sul1-PCR and intI1-PCR was also identified by gel electrophoresis analysis, which further confirmed the advantage of UV/chlorination treatment on DNA damage. Among the radicals produced in UV/chlorination, only the reactive chlorine species (Cl center dot, Cl-2 center dot(-) and ClO center dot) can degrade the target genes. Under the condition of low chlorine dosage, sul1-qPCR was easier to be removed than intI1-qPCR by UV/chlorination. The log reduction of both sul1-qPCR and intI1-qPCR decreased with pH increasing during UV/chlorination. In the presence of sulfamethoxazole, UV/chlorination showed more advantages than direct UV and chlorination in the simultaneous removal of antibiotics, ARBs and ARGs.