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Anthocyanins are the most widely produced secondary metabolites in plants, and they play an important role in plant growth and repro-duction. The nitrogen source is an important factor affecting anthocyanin production, but the nitrogen concentrations on metabolism and the underlying genetic basis remain unclear. In this study, in vitro anthocyanin induction was conducted on Malus spectabilis. The leaf explants were cultivated in media containing different nitrogen concentrations. The results suggested that when the nitrogen contents decreased in limit, the color of leaf explants tued from green to red, and increased anthocyanin accumulation led to a change in phenotype. Furthermore, the con-tent of other flavonoids, such as dihydroquercetin, epicatechin, and catechin, increased under low nitrogen conditions. The transcription levels of the general flavonoid pathway genes, from phenylalanine ammonia lyase (PAL) to anthocyanidin synthase (ANS), were associated with the concentration of corresponding flavonoid compounds and phenotype changes. In particular, the expression level of ANS increased substantially under a low nitrogen treatment, which was significantly and positively correlated with the anthocyanin levels (R2= 0.72, P<0.05). The increased expression pattes of anthocyanin pathway genes were similar to that of the transcription factor MYB10. We further verified MYB10 played an important role in the anthocyanin pathway in leaves of Malus spectabilis. These results suggested that we can improve the desirable oamental plant phenotypes by controlling nitrogen content. This process may offer clues to further development of new agricultural practices.