The study identifies that homologous recombination (HR) and the SOS response are crucial for ciprofloxacin (CIP) persistence in stationary-phase Pseudomonas aeruginosa, while they are dispensable in exponential-phase cultures. Additionally, the SOS response is vital for CIP persistence in stationary-phase E. coli but not in exponential-phase. The roles of HR and SOS in CIP persistence were also verified in a clinical isolate, MRSN 1612.