Croton caudatus is an important species in Dai folk medicine. Some other Croton species, in particular, C. kongensis, C. cascarilloides, C. crassifolius, C. lachnocarpus and C. olivaceus are often marketed as C. caudatus, and thus, the therapeutic effects of C. caudatus are not achieved. The respective morphological features of the plants are similar, and they are not easy to distinguish morphologically from each other. In an attempt to find a method for discriminating among these species, we compared their nuclear ribosomal DNA internal transcribed spacer (ITS) region. Species-specific probes were derived from the ITS region of these species for species identification. This method provides effective and accurate identification of C. caudatus.