Chlorination was reported to have a great potential to increase horizontal gene transfer (HGT) of antibiotic resistance genes (ARGs), which poses a great threat to global human health. Bromide (Br−) and iodide (I−) ions are widely spread ions in water and wastewater. In chlorination, Br− and I− can be oxidized to active bromine and iodine species. The influence of the co-existing different halogen oxidants (chlorine + bromine or iodine species) on HGT of ARGs were rarely investigated. In this study, the conjugative transfer of ARGs between a donor strain E. coli K12 and a recipient strain E. coli HB101 was investigated in chlorination without/with the presence of Br− or I−. Immediately after the addition of sodium hypochlorite, 53–88 % of the dosed chlorine was rapidly consumed, 10 %–42 % fast transformed into organic combined chloramines, and only low levels of free chlorine (0.02–0.8 mg/L as Cl2) left in the diluted cultural medium. Conjugative transfer mediated by the RP4 plasmid was not significantly enhanced in chlorination without the presence of Br− or I−. With the presence of Br− (0.5–5.0 mg/L) or I− (0.05–0.5 mg/L) in chlorination, the co-existing free halogen oxidants and their organic combined ones up-regulated the mRNA expression of the oxidative stress-regulatory gene (rpoS), outer membrane protein gene (ompC), and conjugation-relevant genes (trbBp and trfAp), and caused more damage to cell entirety. As a result, the co-existing reactive halogen oxidants enhanced the HGT of ARGs probably via conjugative transfer and transformation. This study showed that the presence of Br− and I− of common levels in aquatic environment promoted HGT of ARGs in chlorination, thus accelerating the transmission and prevalence of ARGs.