Nuclear DNA content shows extensive intraspecific variation in plants, attributable to changes in levels of repetitive DNA. Since its discovery, repetitive DNA often has been regarded as `junk' or selfish DNA with little or no evolutionary significance at the individual level, except possibly a deleterious role stemming from its over-replication. However, recent works have pointed out that repetitive DNA may have an important impact on phenotypic selection through local or general modifications of gene expression. Phenotypic evolution has typically been studied using quantitative genetic techniques that treat underlying genetic effects as variance components. In previous work, we identified an among population negative correlation between nuclear DNA content variation, attributable to repetitive DNA, and calyx diameter, a phenotypic character with obvious ecological importance, in Silene latifolia. In the present study, we established a negative genetic relation between an AT-biased flow cytometric measure of nuclear DNA content and calyx diameter across lineages that had been subjected to selection for increases or decreases in calyx diameter. This finding suggests that new attention should be directed toward repetitive DNA as a basis for phenotypic variation and evolution.