Technical Abstract: The maize p1 gene encodes a Myb-homologous regulator of red pigment biosynthesis. To investigate the tissue-specific regulation of P1-wr, a white pericarp and red cob allele, maize plants were transformed with constructs combining promoter and cDNA sequences of P1-wr and P1-rr, a red pericarp and red cob allele. Surprisingly, all promoter/cDNA combinations produced transgenic plants with red pericarp and red cob (RR pattern), including a P1-wr promoter driving a P1-wr cDNA. The P1-wr phenotype (WR pattern) was only observed when RR patterned plants from two independent transgenic lines spontaneously produced progeny plants with the WR pattern. This switch in tissue-specific expression correlated with an increase in transgene methylation. A similar association between presence or absence of pericarp pigmentation and degree of DNA methylation was observed for certain natural p1 alleles. p1 alleles were identified that had the gene structure characteristic of standard P1-wr alleles; however, these alleles conferred red pericarp pigmentation and were consistently less methylated than standard P1-wr alleles. Taken together, our results provide evidence that tissue-specific regulation of the P1-wr phenotype is epigenetically controlled.