This　study　investigated　the　effects　of　secondary　chlorination　on　bacterial　regrowth,　microbial　communities　(abundant　and　rare　taxa)　and　bacterial　functions　of　pipe　wall　biofilm　and　bulk　water　in　simulated　secondary　water　supply　system　(SWSS).　Continuous　secondary　chlorination　was　more　effective　than　short-term　secondary　chlorination　to　control　the　bacterial　regrowth　in　both　biofilm　and　water　samples.　Bacterial　diversity　slightly　reduced　after　continuous　secondary　chlorination,　and　19.27%　of　the　total　operational　taxonomic　units　(OTUs)　were　shared　by　biofilm　and　water　samples,　with　Bacillus　as　the　dominant　genus.　Abundant　and　rare　taxa　exhibited　different　community　structures.　Proteobacteria　and　candidate　division　W　PS-1　predominated　in　abundant　and　rare　phyla　were　sensitive　to　chlorine,　while　Firmicutes,　Acidobacteria　and　Bacteroidetes,　exhibited　relative　strong　chlorine　resistance.　The　abundant　genera　in　control　sample　(e.g.,　Bosea,　.Sphingobium　and　Gemmata)　exhibited　poor　tolerance　to　chlorine,　while　Bacillus　in　biofilm　and　Defluvilmonas　in　water　were　the　main　chlorineresistant　genera.　Moreover,　the　composition　of　rare　genera　in　each　sample　was　obviously　different.　Furthermore,　a　total　of　18　potential　pathogens　were　detected　with　Pseudomonas　as　the　dominant　genus,　most　of　which　were　significantly　reduced　after　disinfection.　There　were　mainly　positive　interactions　among　potential　pathogenic　bacteria,　with　Enterococcus,　Legionena　and　Vibrio　as　the　hub　genera　as　revealed　by　network　analysis.　Similar　bacterial　functions　in　both　biofilm　and　water　were　observed　with　metabolism　as　the　predominant　bacterial　function,　while,　human　disease　function　only　accounted　for　1.07%　of　bacterial　functions.　These　results　highlighted　the　importance　of　continuous　secondary　chlorination　for　controlling　biosafety　of　SWSS　and　identified　the　dissimilar　responses　of　abundant　and　rare　bacteria　to　the　disinfection,　as　well　as　the　co-occurrence　patterns　among　potential　pathogens,　improving　our　understanding　of　bacterial　communities　in　SWSS.　(C)　2020　Elsevier　B.V.　All　rights　reserved.