<title>Abstract</title>Proteins KaiA, KaiB and KaiC constitute a biochemical circadian oscillator in the cyanobacterium <italic>Synechococcus elongatus</italic>. It has been reported <italic>kaiA</italic> inactivation completely abolishes circadian oscillations. However, we show here that <italic>kaiBC</italic> promoter activity exhibits a damped, low-amplitude oscillation with a period of approximately 24 h in <italic>kaiA</italic>-inactivated strains. The damped rhythm resonates with external cycles with a period of 24–26 h, indicating that its natural frequency is similar to that of the circadian clock. Double-mutation experiments reveal that <italic>kaiC</italic>, <italic>kaiB</italic>, and <italic>sasA</italic> (encoding a KaiC-binding histidine kinase) are all required for the damped oscillation. Further analysis suggests that the <italic>kaiA</italic>-less damped transcriptional rhythm requires KaiB-KaiC complex formation and the transcription-translation feedback loop, but not the KaiC phosphorylation cycle. Our results provide insights into mechanisms that could potentially underlie the diurnal/circadian behaviors observed in other bacterial species that possess <italic>kaiB</italic> and <italic>kaiC</italic> homologues but lack a <italic>kaiA</italic> homologue.