Technical Abstract: Seed dormancy has been associated with red grain color in cereal crops. The association was linked to the cluster of quantitative trait loci qSD7-1/qPC7 in weedy red rice. This research delimited the cluster to Os07g11020 or Rc encoding a predicted bHLH family transcription factor by intragenic recombinants and provided unambiguous evidence that the association arises from pleiotropy of the regulatory gene. The dormancy gene SD7-1 also enhanced seed weight and abscisic acid (ABA) accumulation during early seed development. Dormancy could be eliminated by a heat treatment, but could not be completely overcome by gibberellic acid or physical removal of the seed maternal tissues. SD7-1 actively expressed early during seed development, promoted expression of key ABA biosynthesis genes to increase ABA content, and activated a conserved gene network for flavonoid biosynthesis to produce the pigments in the lower epidermal cells of the pericarp tissue. Thus, the pleiotropic gene controls the dormancy and pericarp color traits likely by regulating different physiological pathways. The dormancy alleles in weedy red rice differentiated into two groups and the allelic differentiation appeared not to alter their function for seed dormancy. However, detection of SD7-1’s effect on dormancy could be influenced by the genetic background. Of the pleiotropic effects detected, seed dormancy likely contributes most to the adaptation of weedy rice. Pleiotropy also prevents the use of SD7-1 to improve resistance of white pericarp cultivars against pre-harvest sprouting by conventional breeding approaches.