In this study, fruits of the red flesh Malus plant ‘Hongxun 2’ (Malus neidzwetzkyana (Dieck) Langenf.) and green flesh Malus plant ‘Xinye 13-11’ (Malus sieversii (Led.) Roem.) were used as experimental materials. Both of them came from Xinjiang, China, and Malus neidzwetzkyana (Dieck) Langenf. is believed to be a variant of Malus sieversii (Led.) Roem. The components and contents of polyphenols in the peel and pulp of the two kinds of fruit during the development period were detected, and the dynamic changes and differences in the polyphenols between the two kinds of fruit were discussed. The results showed that the total polyphenol content of ‘Xinye 13-11’ was higher in the peel and pulp than that of ‘Hongxun 2’, and the content of peel was higher than that of pulp in the two kinds of fruit. An analysis of five types of polyphenols showed that anthocyanins were only contained in the peel and pulp of ‘Hongxun-2’, and the peel had a higher content than the pulp. Cyanidin 3-O-galactoside was the main anthocyanin component. Four other types of substances, except hydroxycinnamics, were higher in ‘Hongxun-2’ than ‘Xinye 13-11’, while the contents of other substances in ‘Xinye 13-11’ were higher than those of ‘Hongxun 2’. The accumulation of major polyphenol components in the peel and flesh of ‘Hongxun 2’ and ‘Xinye 13-11’ apples was significant in the period before and after 65 days after flowering, and the contents of procyanidin B1 and procyanidin C1 were the highest in this period. In addition to the difference in anthocyanin content between ‘Hongxun 2’ and ‘Xinye 13-11’, the chlorogenic acid content in the peel and pulp of ‘Hongxun 2’ was significantly higher than that of ‘Xinye 13-11’, and the contents of other components were lower than those of ‘Xinye 13-11’. Moreover, based on the components and contents of polyphenol components, this paper supports the viewpoint that Malus neidzwetzkyana (Dieck) Langenf is a separate species to Malus sieversii (Led.) Roem.
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