Abstract: Internal Transcribed Spacer (ITS) 1 and 2 were sequenced for five species of the genus Phyllanthus namely P. emblica, P. reticulatus, P. amarus, P. fraternus and P. urinaria, with a view to identify accurately herbaceous species. All the five species used in the study are medicinally important Affinities among these species were deduced through the help of phylograms generated from their ITS sequences. It was found that internal transcribed spacer 1 showed more potential than internal transcribed spacer 2 in assessing their relationship at molecular level. SCAR markers based on ITS 1 sequences of P. urinaria, P. amarus and P. emblica were designed. All three markers successfully distinguished these species from other closely related species. This is an important tool for identifying plant parts used in ayurvedic medicine.