Abstract A precise and accurate method for the identification and authentication of Phyllanthus niruri L. from P. debilis Klein ex Willd. and P. urinaria L., Phyllanthaceae, was developed using high-performance liquid chromatography. Chromatographic fingerprint analysis was combined with simultaneous quantification of phyllanthin and hypophyllanthin for the developed method. Phyllanthin and hypophyllanthin were successfully separated and quantified under this proposed method. The highest amount of phyllanthin and hypophyllanthin was found in P. niruri compared to P. debilis and P. urinaria. Fingerprint chromatogram of the three Phyllanthus species showed distinct profiles that these may be used to identify and authenticate each Phyllanthus species, which improved by marker compounds present in each species. The combination of chromatographic fingerprint analysis and discriminant analysis was successfully discriminated all three species, including P. niruri adulterated with P. debilis or P. urinaria. The method can be used for the identification and authentication of P. niruri from related species, such as P. debilis and P. urinaria.