The prolamin-box binding factor-1 (pbf1) gene encodes a transcription factor that controls the expression of seed storage protein (zein) genes in maize. Prior studies show that pbf1 underwent selection during maize domestication, although how it affected trait change during domestication is unknown. To assay how pbf1 affects phenotypic differences between maize and teosinte, we compared isogenic lines (NILs) that differ for a maize vs.and teosinte alleles of pbf1. Kernel weight for the teosinte NIL (162 mg) is slightly and significantly greater than that for the maize NIL (156 mg). RNAseq data for developing kernels show that the teosinte allele of pbf1 is expressed at about twice the level of the maize allele. However, RNA and protein assays showed no difference in zein profiles between the two NILs. The lower expression for the maize pbf1 allele suggests that selection may have favored this change, however, how reduced pbf1 expression alters phenotype remains unknown. One possibility is that pbf1 regulates genes other than zeins and thereby a domestication trait. The observed drop in seed weight associated with the maize allele of pbf1 is counterintuitive, but could represent a negative pleiotropic effect of selection on some other aspect of kernel composition.