Introduction The roots of Cissampelos pareira L. var. hirsuta (Buch.-Ham. ex DC.) Forman, Cyclea peltata (Lam.) Hook.f. & Thomson and Stephania japonica (Thunb.) Miers of family Menispermaceae are known as Patha in Ayurveda. They are used in the treatment of various diseases like stomach pain, fever, skin conditions, cardiac pain, etc., among which C. pareira var. hirsuta is the accepted source in Ayurveda (API 2001; Yoganarsimhan 1996). However, the plants of C. peltata are used as Patha in Kerala (Warrier et al. 1994). Authentication of raw medicinal plants is a fundamental requirement for quality assurance in herbal drug markets. Certain rare and expensive medicinal plant species are often adulterated or substituted by morphologically similar, easily available or less expensive species. Pharmaceutical companies procure plant materials from traders, who gather them from untrained collectors in the rural and forest areas. This has given rise to widespread adulteration or substitution, leading to poor quality of herbal formulations (Mehrotra and Rawat 2000). Herbal medicinal products may vary in composition and properties, unlike conventional pharmaceutical products, which are usually prepared from synthetic, chemically pure materials by means of reproducible manufacturing techniques and procedures. Correct identification and quality assurance of the starting material is, therefore, an essential prerequisite to ensure reproducible quality of herbal medicine, which contributes to its safety and efficacy (De Smet 2002; Straus 2002). The morphological, biochemical or histological characteristics employed in the identification are prone to different environmental conditions (Kiran et al. 2010). Limitations of these markers for authentication of herbal drugs have generated a need to develop more reproducible molecular markers for quality control of these medicinal herbs. In view of these limitations, there is need for a new approach that can complement or, in certain situations, serve as an alternative. DNA markers are reliable for informative polymorphisms as the genetic composition is unique for each species and is not affected by age, physiological conditions as well as environmental factors (Chan 2003). DNA-based molecular markers have proved their utility in various fields of science and recently researchers have tried to explore the application of these markers in pharmacognostic characterization of herbal medicine. DNA-based techniques have been widely used for authentication of plant species of medicinal importance. This is especially useful in case of those that are frequently substituted or adulterated with other species or varieties that are morphologically and/or phytochemically indistinguishable. Attempts have been made to compare the source plants of Patha using anatomical and phytochemical markers (Hullatti and Sharada 2007, 2010). But, so far nobody has attempted to characterize these three species at the molecular level. The main objective of the present study is to evaluate the source plants of Patha using inter simple sequence repeat (ISSR) markers for the accurate identification of C. pareira var. hirsuta, C. peltata and S. japonica.