Morphological resemblance among Cymbopogon distans species and their adulterants which are procured from different markets in the form of dried or fresh plant tissues represents a serious problem for quality and safety of medicinal plants, as it supports frauds for substitution. In order to assure the quality control of C. distans species, DNA barcode, microscopic identification and High Performance liquid chromatography (HPLC) fingerprint were synergistically used to discriminate C. distans from its adulterants. In this work, the internal transcribed spacer 2 (ITS2) was chosen for distinguishing C. distans from their usual adulterants from 5 provinces of China. Sequences were obtained after removal of the 5.8S and 28S sections. A multiple sequence alignment was finalized. Results exhibited that ITS2 performed well, with 100% of genera being accurately distinguished. Additionally, finding indicates that the upper epidermis in leaf of C. distans was composed of one layer of wide elongated cells called Bulliform cells whereas in C. distans the upper epidermis consist of one layer cell, thus these feactures are very important for the anatomy identification. The HPLC fingerprint method was also developed, the similarities of 6 batches of C. distans samples were all more than 0.93, indicating that the samples from different geographical origins shared similar HPLC fingerprints. And the similarities between C. distans, C. citratus, C. flexuosus and Imperata cylindrica were all less than 0.93, suggesting that there was significance difference between C. distans and its adulterants. Finally, it was concluded that the DNA barcode, HPLC fingerprint and microscopic methods could effectively authenticate the quality of C. distans from their adulterants and can provide accurate and reliable information to tackle the complex quality issue of C. distans in markets. This is the first report of detailed analysis of the C. distans for effective quality and safety.