One of the main targets of the vesicular glutamate transporter type 3 (vGluT3)-expressing median raphe neurons, is the dorsal hippocampus, a key node of the brain’s episodic memory circuit. We uncovered previously that the raphe-hippocampal glutamatergic connection selectively and highly efficiently activates certain types of hippocampal inhibitory neurons at very short latency. However, the function of this powerful inhibition-targeting modulation is still elusive. In this study, we combined the selective tagging of either vGluT3 MR neurons or their hippocampus-projecting subgroup and high-density silicone probe recording of both MR and dorsal CA1 activity in head-fixed, awake mice. During the recording, the animals had to run on a disc while exposed to both aversive and rewarding stimuli at pre-determined locations. We utilized both excitatory and inhibitory tagging by Channelrhodosin2 and ArchaerhodopsinT, respectively. According to our results, activations of vGluT3 neurons by 25 Hz pulse train triggers reorganization of place cells’ activity. More interestingly, inhibition of median raphe vGluT3 neurons interferes both with coding of the reward place and with the aversive stimulus-evoked response of pyramidal cells. Hence, the raphe-hippocampal glutamatergic pathway may convey a saliency signal to the dorsal CA1 circuit.