The B gene encodes a transcription factor of the basic helix-loop-helix class, which controls the synthesis of the anthocyanin pigments in maize. This gene, as well as the highly homologous R gene family, displays extensive allelic variation in that different alleles cause distinct distributions of anthocyanin pigments in different tissues and at different developmental times. The analysis of the expression of two B alleles, with distinct tissue-specific patterns of anthocyanin synthesis in plant and seed tissues, demonstrates that the amount of B transcripts correlates with the accumulation of anthocyanins in the various tissues. The comparison of the genomic clones for the two alleles reveals high sequence identity in the coding and 3'-flanking regions (98% and approximately 90%, respectively). In contrast, the most 5' region of their mRNAs and the 5'-flanking sequences share no significant sequence identity. This result suggests that the alleles diverged from each other by complex genome rearrangements rather than by simple base pair substitutions. We have used the high velocity microprojectile transformation assay to demonstrate that the differential expression of the two alleles in the seed is determined by their 5' variant sequences. Thus, the variation in tissue-specific anthocyanin synthesis in plants with these different B alleles is controlled at the level of B gene expression.