Desmodium caudatum (Thunb.) DC, is an ever-green plant widely used in the central and southern China with great economic value for their medical values on fever, dysentery, gastroenteritis, rectal prolapse, snake bites, mastitis, and boils carbuncle. Despite its extensive uses as a traditional Chinese medicine, no systematic research on the identification of Desmodium caudatum has been reported. In this study, traditional pharmacognostical identification including the botanical origin and morphological characters, medicinal material characters, microscopic characters, physicochemical parameters determination and phytochemical screening, and DNA barcoding analysis were employed to establish an accurate and effective identification system of Desmodium caudatum. In addition, the molecular pharmacognosy study was adopted in order to identify the samples more accurately. The ITS loci of the nuclear genome and psbA-trnH loci of the chloroplast genome were selected and evaluated, which were the most variable loci. The study will be beneficial to the development of the quality standard and the identification of species.