Abstract:The Indigofera szechuensis complex contains nine species: I. szechuensis, I. pendula, I. hancockii, I. franchetii, I. delavayi, I. lenticellata, I. rigioclada, I. calcicola and I. heterantha. In this study, we conducted morphological and ITS variation analyses of 240 samples from 31 populations. Analysis of means showed that the nine species of the I. szechuensis complex mainly differed in leaflet size and inflorescence length. Principal component analysis indicated that the maximal leaf length, leaflet trichomes, anther trichomes and leaflet length to width ratio were the main interspecific morphological differences. Phylogenetic analysis based on ITS sequences indicated that interspecific relationships within the I. szechuensis complex were not resolved, except for I. delavayi. We concluded that these eight species of the I. szechuensis complex might be undergoing species differentiation caused by the complex habitats and geological history of the Hengduan Mountain region.