The lateral habenula (LHb) is viewed as a relay between the limbic system, the basal ganglia (BG), and monoaminergic neurons of the midbrain. If a prominent role has been evidenced in BG-mediated functions such as value-based decision-making, very little is known about the involvement of the LHb in limbic functions such as memory processing. In the present study, we used two pharmacological approaches-LHb reversible inactivation with intra-LHb infusion of muscimol, an agonist of the GABA-A receptor, or blockade of excitatory inputs with intra-LHb infusion of 6-cyano-7-nitroquinoxaline-2,3-dione (CNQX), an antagonist of the glutamatergic AMPA receptor-to investigate the involvement of the LHb in encoding, consolidation, and retrieval of spatial memory in the water maze (WM) in rats. We found that intra-LHb infusion of muscimol or CNQX prevented encoding and retrieval, but not consolidation of spatial information. In addition, muscimol but not CNQX induced impairments during a cued version of the WM task, and marked anxiety in the elevated plus maze. These results confirm the involvement of the LHb in higher cognitive functions. They further suggest a dichotomy between the role of glutamatergic and other inputs to the LHb in hippocampus-dependent memory processing, as well as in emotional aspects of goal-directed behaviors.