Abstract: A few individuals with intermediate morphology always appear in the sympatric distributions of Gentiana straminea and G. siphonantha. These intermediate individuals were hypothesized to be the hybrids of two species after a careful evaluation of their morphological characters. To test this hypothesis, the sequence comparison of the internal transcribed spacer ( ITS) regions of nuclear ribosomal and trnS (GCU)- trnG (UCC) intergenic spacer region of the chloroplast DNA from Gentiana straminea, G. siphonantha, and the putative hybrids was performed. The results suggested that most
intermediate individuals were the natural hybrids between G. straminea and G. siphonantha. In addition, we examined the sequence variation among the individuals of both parent species and provided the possibility leading to the incongruent identification to some individuals by morphology and molecular evidences respectively. The intraspecific diversification of DNA fragments within both parent species and their high variability in hybrid swarms probably resulted from chloroplast genome recombination and incomplete lineage sorting during the early stage of speciation origin of parent species.