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Objective: To distinguish the difference among the Clinacanthus nutans (Burm. f.) Lindau (C. nutans) and Clinacanthus siamensis Bremek (C. siamensis) by assessing pharmacognosy characteristics, molecular aspect and also to evaluate their anti-herpes simplex virus (HSV) type 1 and type 2 activities. Methods: Macroscopic and microscopic evaluation were performed according to WHO Geneva guideline. Stomatal number, stomatal index and palisade ratio of leaves were evaluated. Genomic DNA was extracted by modified CTAB method and ITS region was amplified using PCR and then sequenced. Dry leaves were subsequently extracted withn-hexane, dichloromethane and methanol and antiviral activity was performed using plaque reduction assay and the cytotoxicity of the extracts on Vero cells was determined by MTT assay. Results: Cross section of midrib and stem showed similar major components. Leaf measurement index of stomatal number, stomatal index and palisade ratio of C. nutans were 168.32±29.49, 13.83±0.86 and 6.84±0.66, respectively, while C. siamensis were 161.60±18.04, 11.93±0.81 and 3.37±0.31, respectively. The PCR amplification of ITS region generated the PCR product approximately 700 bp in size. There were 34 polymorphisms within the ITS region which consisted of 11 Indels and 23 nucleotide substitutions. The IC50 values of C. nutans extracted with n-hexane, dichloromethane and methanol against HSV-1 were (32.05±3.63) μg/mL, (44.50±2.66) μg/mL, (64.93±7.00) μg/mL, respectively where as those of C. siamensis were (60.00±11.61) μg/mL, (55.69±4.41) μg/mL, (37.39±5.85) μg/mL, respectively. Anti HSV-2 activity of n-hexane, dichloromethane and methanolC. nutans leaves extracts were (72.62±12.60) μg/mL, (65.19±21.45) μg/mL, (65.13±2.22) μg/mL, respectively where as those of C. siamensis were (46.52±4.08) μg/mL, (49.63±2.59) μg/mL, (72.64±6.52) μg/mL, respectively. Conclusions: The combination of macroscopic, microscopic and biomolecular method are able to authenticate these closely related plants and both of them have a potency to be an anti-HSV agent.