Using megagametophyte (maternal haploid) and embryo (diploid) tissues of incense-cedar seeds, the expression of one of three malate dehydrogenase (MDH) loci was found to be influenced by a second, unlinked, modifier locus. Whereas alleles of the affected structural locus are codominant, the modifier alleles show dominance. The action of the modifier, limited to 1 of 28 structural loci examined, results in a shift of electrophoretic mobility detectable in conventional starch gels. Both the structural and the modifier MDH loci are polymorphic in all populations surveyed. Studies of genetic variation in natural populations made without rigorous genetic analysis may not detect such modification. By misinterpreting the genetic basis of enzyme phenotypes, such undetected modification can result in overestimates of genetic diversity in natural populations and can cause an apparent excess of homozygotes relative to expectations. These effects on allele and genotype frequency estimates are dependent on the levels of polymorphism at both the structural and the modifier loci. Using procedures common to many surveys of electrophoretic variation, the frequency of a recessive modifier allele could be as high as 0.3 before being detected.