Daqingye and Banlangen are commonly used Chinese medicinal materials derived from the leaves and roots of Isatis indigotica Fort., respectively, which clinical effects have been confirmed by many studies in recent years. However, many problems have arisen concerning the quality and identity of materials sold in the market under these two names. Thus, the identification of Daqingye and Banlangen has drawn public attention. In this work, transverse sections of Daqingye and Banlangen from I. indigotica Fort. and two easily confused species, namely Baphicacanthus cusia (Nees) Bremek. and Clerodendrum cyrtophyllum Turcz., were investigated with normal light and fluorescence microscopy. The distinguishing features were 7-9 vascular bundles, cystoliths and nonglandular hairs in the leaves of I. indigotica, B. cusia, and C. cyrtophyllum, respectively. The Banlangen could be distinguished according to the characteristics of parenchymous cells, cystoliths, and stone cells. Moreover, the fluorescence features of Daqingye and Banlangen investigated in this study can provide direct points for differentiating those samples. Importantly, whether the crude drugs were decocted could be easily identified by their different fluorescence features, which can ensure their quality in clinical application. This is the first report to distinguish the three species that are commonly found in the market sold as Daqingye and Banlangen by normal light and fluorescence microscopy. This work indicates that the combination of normal light and fluorescence microscopy could be powerful, convenient, and economical for authenticating Daqingye and Banlangen from the three species, including crude drugs and decoction dregs.