The maize P gene encodes a Myb-homologous transcriptional regulator of flavonoid pigmentation in floral organs, and different P gene alleles condition precise tissue- and organ-specific pigmentation patterns. To determine the molecular basis for allele-specific expression patterns, we have isolated and compared two natural alleles of the P gene which differ in expression, structure and copy number. The P-rr allele is associated with pigmentation of most floral tissues and contains a single copy of the P gene. In contrast, the P-wr allele restricts pigmentation to a subset of floral tissues, and is composed of six gene copies arranged in a tandem head-to-tail array. Each of the six repeats contains a single P gene, including regulatory and coding sequences. Despite the six-fold tandem repetition of P-wr gene copies, P-wr mRNA levels in kernel pericarp are much reduced compared to mRNA levels from the single-copy P-rr gene. Moreover, the P-wr multicopy complex is hypermethylated relative to P-rr. Thus, maize P gene alleles may represent a natural system for studying the effects of methylation and gene copy number on tissue-specific gene expression. We discuss the possibility that somatic pairing of repeated gene copies may be involved in regulating gene expression.