Fabaceae is a huge family that contains a large number of medicinal plants, many of which are commonly used in Chinese traditional medicine. However, traditional taxonomy has not been able to meet the complicated demands of species discrimination within Fabaceae. Thus, we employed a famous DNA barcode, the psbA-trnH region, to discriminate commonly used medicinal species of the family Fabaceae. Here, the psbA-trnH regions derived from 152 samples were amplified. These samples represented 104 Fabaceae medicinal species from 60 genera, including 25 authentic Fabaceae species listed in the Chinese pharmacopoeia and common adulterant species. The results indicate that the psbA-trnH region performed well in terms of its universality and high variability in length and composition. Species discriminative power analysis of the psbA-trnH region showed that 91.3% of species could be identified successfully by the BLAST1 method in conjunction with the nearest distance method. And, the species resolution rate of the TaxonGap method exceeded 93%. The results provide support for the use of the psbA-trnH plastid region as a sensitive marker to the authentication of Fabaceae medicinal plants.