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The monoaminergic neurotransmitter serotonin (5-HT) is one of key regulators of brain states, with reduced release during sleep. Serotonin is also known to powerfully suppress hippocampal theta oscillations in the awake brain. During non-rapid eye movement (NREM) sleep, brief theta bursts (TBs) have been identified in the cortex and are implied in neuronal reactivation. We investigated whether and how the 5-HT system modulates these cortical TB events during NREM sleep. Using simultaneous EEG/EMG recordings and fiber photometry to monitor 5-HT neuronal activity and extracellular 5-HT concentration, we found that cortical TB occurrence is inversely correlated with the serotonergic tone: calcium activity in serotonergic neurons and extracellular 5-HT levels gradually decreased before TBs, suggesting that TBs are most probable when 5-HT activity is low. Then, we demonstrated that optogenetic activation of dorsal raphe 5-HT neurons during NREM sleep significantly decreased the rate of TBs and reduced theta power in the absence of sleep-to-wake transitions. Conversely, pharmacological inhibition of the 5-HT system using an inhibitory 5HT1A receptor agonist increased the rate of TBs during NREM sleep. Furthermore, we examined TB-related hippocampal activity and found that the major excitatory neuronal populations in the dentate gyrus (DG), including granule cells and mossy cells, significantly increased calcium activity before the TBs. This TB-related DG activity increase was suppressed when the 5-HT system was pharmacologically inhibited. These results indicate that serotonin suppresses cortical theta bursts and that a low 5-HT state is essential for TB-related hippocampal activity during NREM sleep, defining a critical neuromodulatory gating mechanism for sleep-specific brain oscillation associated with memory processing.