This research was conducted in order to understand the hybridization between Quercus aliena Blume and Q. serrata Murray in Korea which show wide range of morphological variations within species and interspecific variations of diverse overlapping characteristics caused by hybridization. Morphological analysis (principal components analysis; PCA) of 116 individuals representing two species and their intermediates were performed. As a result, two species were clearly distinguished in terms of morphology, and intermediate morpho-types assumed to be hybrids between the two species were mostly located in the middle of each parent species in the plot of the principal components analysis. There was a clear distinction between two species in trichome distribution pattern which is an important diagnostic character in taxonomy of genus Quercus, whereas intermediate morpho-types showed intermediate state between two species’ trichome distributions. Forty-two individuals representing two species and their intermediates were examined for leaf flavonoid constituents. Twenty-three flavonoid compounds were isolated and identified: They were glycosylated derivatives of flavonols, kaempferol, quercetin, isorhamnetin and myricetin. The flavonoid constituents of Q. aliena were five glycosylated derivatives: kaempferol 3-O-galactoside, kaempferol 3-O-glucoside, quercetin 3-O-galactoside, quercetin 3-O-glucoside, and Isorhamnetin 3-O-glucoside. The flavonoid constituents of Q. serrata had 20 diverse flavonol compounds including five flavonoid compounds found in Q. aliena. It was found that there is a clear difference in flavonoid constituents of Q. aliena and Q. serrata. Flavonoid chemistry is very useful in recognizing each species and putative hybrids. The flavonoid constituents of intermediates were a mixture of the two species’ constituents and they generally showed similar characteristics to morpho-types. The hybrids between Q. aliena and Q. serrata showed morphologically and chemically diverse characteristics and it is assumed that there are frequent interspecific hybridization and introgression.