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Differences in anthocyanin accumulation and morpho-anatomical features in skin of apple cultivars (Malus domestica Borkh cv. Starkrimson and Golden Delicious) were compared during the color formation at two habitats (Maoxian and Ya’an, China) in the low latitude zone of apple cultivation. Anthocyanin content in the skin of both cultivars under the semi-arid, cool, and high-irradiant habitat of Maoxian was higher than that under the moist, warm, and low-irradiant habitat of Ya’an. Likewise, the contents of reducing and non-reducing sugar, and the activity of phenylalanine ammonia-lyase (PAL, E.C.4.3.1.5) were also higher, but contents of malic acid and water were lower in skin of the two cultivars of Maoxian. Within the same habitat, higher content of anthocyanin and activity of PAL were found in skin of ’starkrimson’ apple than ’Golden Delicious’ apple, but no difference in the contents of reducing and non-reducing sugar, malic acid, and water. The analysis of morphological and anatomical features showed that the two apple cultivars in Maoxian had smaller and fewer lenticels, thicker cuticle, longer and thinner epidermal cells, and longer and thinner sub-epidermal cells with more layers than those in Ya’an. Regression analysis showed that PAL activity, reducing sugar content, and lenticel density, as well as cuticular thickness, and cell length and thickness of epidermis, were associated with anthocyanin accumulation in apple skin. (C) 2003 Elsevier B.V. All rights reserved.