Phyllanthus species have been used as traditional medicine for a long time that they can be used for the treatment of digestion, jaundice and renal calculus. Among them P.rheedei (rare) and P.scabrifolius (endemic to southern peninsular India) which are almost identical in exomorphological characteristics but differ in a few micro-morphological attributes. These two medicinally potential species belonging to Phyllanthaceae were reputed for hepatoprotective activity against Hepatitis B virus and also little known and under explored in the field of Phytomedicine. Preponderance of other herbaceous Phyllanthus spp., often leads to deliberate adulteration or substitution, lowering the efficacy of medication. Morphological attributes are inadequate for distinguishing these two test species. Hence, the present study was focused on to evaluate the morphological, organoleptic and anatomical characteristics that can be used for identification and discrimination of species. Established pharmacognostic profile of crude drug samples taken for further study and also for the future conservation strategy. Microscopic observation of Phyllanthus species revealed the presence of anisocytic and paracytic type of stomata found in P.rheedei while only paracytic type in P.scabrifolius. The aqueous leaf extracts of P.rheedei and P.scabrifolius were subjected for their antimicrobial activity by disc diffusion method against both Gram +ve, Gram –ve pathogenic bacteria and fungal strains. It was observed that root extract of P.rheedei exhibited significant antimicrobial activity than that of P.scabrifolius.