The genus Sida L. (family: Malvaceae) is widely used in India and many other countries including China, South East Asia, Africa and South America for treating various neurological disorders and for improving general health and vigour. However, as with many other herbal medicines, it is believed that the Sida products sold in the market may be adulterated with other related or unrelated plant species. In this study, we investigate species adulteration in the raw herbal trade of Sida natural health products (NHPs) in southern India. DNA barcoding was used as a tool to identify the ingredients in the NHPs. A biological reference material (BRM) library for Sida and closely related species was developed using taxonomically authenticated species. DNA barcodes for the species were developed using one nuclear (ITS) and two chloroplast regions (matK and psbA-trnH). The psbA-trnH and ITS region were found to effectively discriminate all species with an interspecific distance of 0.133 and 0.149 and intra-species distance of 0.007 and 0.015 respectively. These DNA barcodes were used to identify the ingredients in raw Sida herbal products obtained from 10 markets in Southern India. Our study indicated that species adulteration in the market samples is rampant especially in case of Sida cordifolia, where all the market samples analyzed were Sida acuta. We discuss the results and the need for a robust herbal drug authentication system to regulate the quality in raw herbal trade market.