Chlorine disinfection is a commonly used disinfection process in wastewater treatment, but its effects on the indigenous bacterial community in treated wastewater have not been fully elucidated. In this study, secondary effluent samples collected in four wastewater treatment plants (WWTPs) were selected for chlorine disinfection. Shifts in the bacterial community compositions in secondary effluent samples upon chlorine disinfection, both immediately and after 24 h of storage, were investigated using Illumina MiSeq sequencing combined with propidium monoazide (PMA) treatment. The results showed that the phylum Proteobacteria was sensitive to chlorine, with the relative proportions of Proteobacteria decreased from 39.2 to 75.9 % in secondary effluent samples to 7.5 to 62.2 % immediately after chlorine disinfection. The phylogenetic analysis indicated that the most dominant genera belonging to Proteobacteria were sensitive to chlorine. In contrast, the phyla Firmicutes and Planctomycetes showed a certain resistance to chlorine, with their relative proportions increasing from 5.1 to 23.1 % and 0.8 to 9.3 % to 11.3 to 44.6 % and 1.5 to 13.3 %, respectively. Most dominant genera belonging to Firmicutes showed resistance to chlorine. A significant reduction in the richness and diversity of the bacterial community was observed after 24 h of storage of chlorinated secondary effluent. During the 24-h storage process, the relative proportions of most dominant phyla shifted in reverse from the changes induced by chlorine disinfection. Overall, chlorine disinfection not only changes the bacterial community compositions immediately after the disinfection process but also exerts further impacts over a longer period (24 h).