The present study explored the possibility that cholinergic and GABAergic systems of medial septum (MS) might influence acquisition of memory by regulation of acetylcholine (Ach) and γ-aminobutyric acid (GABA) receptors function in hippocampus and vice versa. The step-through passive avoidance (PA) task was used. The results showed that pre-training intra-MS/CA1 administration of nonselective muscarinic Ach antagonist, scopolamine (0.5, 1 and 2 μg/rat) and GABA(A) receptor agonist, muscimol (0.01 and 0.02 μg/rat) impaired, while acetylcholinesterase inhibitor, physostigmine (0.5 and 1 μg/rat) and GABA(A) receptor antagonist, bicuculline (0.25 μg/rat) improved memory acquisition. Moreover, intra-CA1/MS administration of a subthreshold dose of muscimol or bicuculline increased and reversed the impairment induced by scopolamine in MS/CA1 respectively (cross injection). Also, the result revealed that, intra-CA1/MS administration subthreshold dose of muscimol reduced improvement of memory induced by physostigmine in the MS/CA1, respectively (cross injection). On the other hand, subthreshold dose of bicuculline in CA1/MS did not alter memory improvement induced by physostigmine in the other site (MS/CA1). In conclusion, both cholinergic and GABAergic systems not only seem to play a role in the modulation of memory in the MS and CA1 but also to have a complex interaction.