Nepeta depauperata belongs to the Lamiaceae family and is one the Persian endemic plants which has not been investigated biologically. In the present paper we had focused on the assessment of the antibacterial and antifungal activities of the total methanolic extract and different sub-fraction of the flowering aerial parts of it. The Antibacterial and antifungal activities were investigated by cup plate method and disc diffusion assay, respectively. The minimum inhibitory concentrations and minimum bactericidal concentrations of the active extract or subfraction were determined by micro plate dilution method. The crude extract and chloroform sub-fraction of N. depauperata had inhibition activity on the growth of Staphylococcus aureus, Bacillus subtilis and Pseudomonas aeruginosa while no antibacterial activity observed against Staphylococcus epidermidis, Escherichia coli and Salmonella typhi. It was concluded from the antifungal assay that just the yeast C. albicans, showed a high sensitivity to all the extract and related sub-fractions. No activity was seen against Aspergillus niger, A. fumigatus, A. flavus and Fusarium oxysporum. These findings demonstrate that the N. depauperata is effective against S. aureus, B. subtilis and P. aeruginosa and could be a natural source of effective natural antifungal compounds against C. albicans.