Two representative low nucleic acid-content (LNA) bacterial strains, Polynucleobacter sp. CB and Sphingopyxis sp. 15Y-HN, and two commonly used microbial indicators of drinking water disinfection efficiency, Escherichia coli and Pseudomonas aeruginosa, were used to investigate the effects of chlorine disinfection. LNA bacteria were found to be more tolerant than microbial indicator strains at the same free chlorine concentrations in batch experiments. Three-stage chlorination experiments were carried out for two strains (15Y-HN and E. coli K12) to compare their responses to long-term chlorine exposure. Results from the first stage (increasing chlorine exposure from 0.0 to 0.6 mg/L and 1.2 mg/L for strain K12 and strain 15Y-HN, respectively) showed the rate constants of 99% cell damage were 10-fold lower for strain 15Y-HN than for strain K12. A second regrowth stage at low free chlorine concentrations (< 0.3 mg/L for 140 h) facilitated the regrowth of chlorine-resistant populations of strains 15Y-HN and K12 in the presence of assimilable organic carbon (AOC). In the third stage, during which bacteria were exposed to increasing chlorine from 0.0 to 0.5-0.6 mg/L, strain 15Y-HN was maintained at 80% and 105 cells/mL of intact cells whereas strain K12 was completely damaged. The overall results demonstrated that representative LNA bacteria exhibit strong resistance and resilience to chlorine under low AOC conditions, which should be taken into consideration in disinfection processes.