A putative natural hybrid in Ligularia Cass., which is morphologically intermediate between L. paradoxa Hand.-Mazz. and L. duciformis (C. Winkl.) Hand.-Mazz., was found on Mt. Maoniu in northwestern Yunnan, China. We employed analyses of morphology, seed vigor, somatic chromosome numbers, meiotic behavior of chromosomes, inter-simple sequence repeat (ISSR) markers, and trnL-F sequencing to test the hypothesis that the unidentified taxon is a natural interspecific hybrid between L. paradoxa and L. duciformis. Examination of morphological characters demonstrated the intermediacy of the putative natural hybrid between L. paradoxa and L. duciformis. Seed germination of the putative natural hybrid was absent, and no embryo was found in seeds of the putative natural hybrid. The meiotic behavior of the putative natural hybrid was abnormal. Among 10 ISSR primers that we tested in all three taxa, four primers produced different ISSR markers between the putative parents. The putative natural hybrid shared all ISSR markers of the putative parents. However, no taxon-specific band existed in the samples of the putative natural hybrid. The data from ISSR markers are concordant with morphology in implicating L. paradoxa and L. duciformis as parents of the putative natural hybrid. Ligularia paradoxa was determined as the female parent of this natural hybrid by nucleotide sequence from the chloroplast trnL-F region. Therefore, this taxon is confirmed to be a natural hybrid between L. paradoxa and L. duciformis and is described herein.