Pterygiella, a genus endemic to southwestern China, belongs to hemiparasitic rhinanthoid Orobanchaceae. Since P.bartschioides was segregated as an independent genus of its own, i.e. Xizangia, the genus was treated to include four species, P.duclouxii, P.nigrescens, P.cylindrica, and P.suffruticosa. However, the discriminative characters are obscure among these species, and the delimitation of the two varieties in P.duclouxii remains problematic. To revise the taxonomy of the genus, thirteen populations from the four species were collected for both morphometric and molecular systematic analyses. Principal component analysis (PCA) and cluster analysis via unweighted pairgroup method with an arithmetic average (UPGMA) were used. In addition, four chloroplast sequences (i.e., atpBrbcL, psbAtrnH, trnDtrnT and trnStrnG) and nuclear ITS region were studied. The results showed that Pterygiella includes only three species, namely P.nigrescens, P.duclouxii, and P.cylindrica, while P.suffruticosa should be merged into P.cylindrica as a variety. The previous delimitation of the two varieties within P.duclouxii was probably caused by imperfect analysis of morphological characters. Thus, a lectotype was designated for P.duclouxii and the plants formerly treated as P.duclouxii that bear eglandular stem hairs should be put into P.nigrescens, while the individuals with glabrous stem should remain in P.duclouxii. A new key to the three species in the genus reflecting the results of this study was presented, and a taxonomic revision was given.