One of the most important factors determining apple [ Malus pumila P. Mill.] market acceptance is peel color. Most apple cultivars (e.g. 'Royal Gala') produce fruit with a defined fruit pigment pattern, but in the case of 'Honeycrisp' apple, trees can produce fruits of two different kinds: striped and blushed. The causes of this phenomenon are unknown. We compared 'Honeycrisp' fruit from trees that were propagated from buds occurring on branches carrying only blushed or only striped fruit and 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. We have also shown that striped areas of 'Honeycrisp' and 'Royal Gala' are due to sectorial increases in anthocyanin concentration. Transcript levels of the major biosynthetic genes and MdMYB10, a transcription factor that upregulates apple anthocyanin production, correlated with increased anthocyanin concentration in stripes. However, changes in the promoter and coding sequence of MdMYB10 do not correlate with skin pattern in 'Honeycrisp' and other cultivars differing in peel pigmentation patterns. A survey of methylation levels throughout the coding region of MdMYB10 and a 2.5 kb region 5' of the ATG translation start site indicated that an area 900 bp long, starting 1400 bp upstream of the translation start site, is highly methylated. Comparisons of methylation levels of red and green stripes indicated that the degree of methylation of the MdMYB10 promoter is likely to be associated with the presence of stripes in these cultivars, with red stripes having lower methylation levels. Methylation may be associated with the presence of a TRIM retrotransposon within the promoter region, but the presence of the TRIM element alone cannot explain the phenotypic variability observed in 'Honeycrisp'. We suggest that methylation in the MdMYB10 promoter is more variable in 'Honeycrisp' than in 'Royal Gala', leading to more variable color patterns in the peel of this cultivar.