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One of the most important factors determining apple (Malus pumila P. Mill.) market acceptance is peel color. Coloring of ‘Honeycrisp’ fruits can adopt two patterns: blushed or striped. This is an unusual phenomenon in apple. The objective of this study was to compare ‘Honeycrisp’ fruit from trees that were propagated from buds occurring on branches carrying only blushed or striped fruit. We concluded that blushed trees tend to produce a higher percentage of blushed fruit than striped trees, indicating a mechanism conserved through cell division. The percentage of blushed fruit on any given tree changed from year to year. Blushed and striped fruit occurred together on the same branch, and even on the same spur, with fruits located in the outer canopy being more likely to be striped. Higher crop loads were associated with a lower percentage of blushed fruit on the tree. Blushed and striped fruit do not consistently differ in their maximum pigment accumulation before ripening. The comparison of average hue angle for the whole peel at harvest indicates that blushed fruit are redder on average. Stripes were caused by reduced anthocyanin accumulation in certain portions of the peel and not by deeper localization. We speculate that an epigenetic mechanism regulates the pattern of anthocyanin accumulation in ‘Honeycrisp’ apple. Increased production of blushed, redder apples may be achieved through clonal selection and crop load regulation. A software tool for efficient relative color evaluations was developed and is freely available to the community.