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Based on the presence of intermediate morphological characters, such as serrated leaf margins and flower structures, Ilex xwandoensis was initially described as a putative natural hybrid between I. cornuta and I. integra, and was formally described as a new hybrid species, I. xwandoensis C. F. Mill., and M. Kim. However, using molecular markers generated via random amplified polymorphic DNA (RAPD), we have now discovered hybridization in' populations' of the I. xwandoensis complex collected from Wando and Jeju Islands, Korea. Marker bands of the putative' parent taxa also were found in some populations of I. xwandoensis, confirming its hybrid origin. Morphological variability within and among those populations was confirmed by model-based clustering methods, using multilocus genotype data; Phenograms generated from RAPD bands indicated, that some accessions of I. xwandoensis clustered with one of the parental species. This implied the occurrence of hybridization and recurring backcrosses of the hybrid to both parents, resulting in various hybrid derivatives because of the segregation and recombination of traits. Ilex xwandoensis was more closely related to I. cornuta than to I. integra, suggesting that it backcrossed more with the former than with the latter.