Antimicrobial activity of methanolic extracts of Chamaecyparis obtuse (CO), Chrysanthemum boreale (CB) and Cryptomeria japonica (CJ) against four bacteria (Staphyloscoccus aureus, Bacillus cereus, Escherichia coli and Yesinia enterocolitica) was evaluated by a disk diffusion method. Anti-human rhinovirus (HRV) 3 activity and cytotoxicity of them were evaluated by a cytopathic effect reduction method. The methanolic extracts of CB showed antimicrobial activity against tested four microorganisms with diameter of inhibition zones from 0.5 to 2.0 mm. The other extracts showed weak antimicrobial activity against Bacillus cereus and didn't exhibit antimicrobial activity against Escherichia coli and Yesinia enterocolitica. The antiviral assays demonstrated that methanolic extracts of CO and CJ possessed strong antiviral activity against HRV3 with 77.8% and 93.7%, respectively, at a concentration of 100 μg/mL with no cytotoxicity. However, methanolic extracts of CB did not show anti-HRV3 activity. Therefore, the antimicrobial of CB and antiviral activity of CO and CJ will be further investigate in preventing bacteria pathogens or HRV3-mediated injuries in pathological situations.