In present paper, the properties of molecular authentication combined with the fingerprints of high performance liquid chromatography (HPLC) were validated by analyzing ten batches of Fructus Evodiae samples (the dried nearly ripe fruit of Evodia rutaecarpa (JUSS.) BENTH., Evodia rutaecarpa (JUSS.) BENTH. var. officinalis (DODE) HUANG or Evodia rutaecarpa (JUSS.) BENTH. var. bodinieri (DODE) HUANG). The results of this investigation show that the similarities of internal transcribed spacer (ITS) sequences were almost 100% in Evodia rutaecarpa (JUSS.) BENTH. var. bodinieri (DODE) HUANG, 97% in Evodia rutaecarpa (JUSS.) BENTH., and 96% in Evodia rutaecarpa (JUSS.) BENTH. var. officinalis (DODE) HUANG. The percentage of identity between the two groups of Evodia rutaecarpa (JUSS.) BENTH. var. bodinieri (DODE) HUANG and Evodia rutaecarpa (JUSS.) BENTH. var. officinalis (DODE) HUANG is almost 96%, but the identity among the group of these three species is only 73%. The results show that Fructus Evodiae comes from three species respectively. The fingerprints of HPLC show that Fructus Evodiae revealed 20 major common peaks. And the three species have almost the same chemical constituents. ITS sequence fingerprint combining the fingerprint of HPLC can not only be developed to identify and distinguish the three species in detail, but also can be used for optimizing location where Fructus Evodiae has much higher bioactive constituents and yield.