Seeds are coated with pigments presumably to promote plant adaptation. To understand the adaptive mechanisms of seed pigment traits, allelic variants of the red (Rc/rc) and purple (Pb/pb) pericarp color genes were assembled into the same genetic background to identify the trait development patterns and pleiotropies of the loci on seed flavonoids, dormancy and germination in rice (Oryza sativa). Non-allelic recombination and epistasis of the loci dictated four patterns of the trait development from 5 to 40 days post anthesis (DPA). The Rc- and Pb-controlled pigments were synthesized in the same lower epidermal cells but compartmented in the cells and lignified wall area, respectively, after 10 d. Four flavan-3-ols (catechin, epicatechin and their dimeric procyanidins) and anthocyanins (AC) were detected in the Pb and Rc systems, respectively, with catechin being most abundant. Both genes affected seed primary dormancy, and imbibition and germination velocities of the dormancy-released seeds. Additive effects of the loci contributed most to the variances for all the pleiotropic traits, the development time and its interaction with the additive components influenced the flavonoid contents, and the additive-by-additive epistasis modified the AC content and dormancy level. Thus, seed pigment traits influence plant adaptation likely through a series of pleiotropies, including the coat structure, enhanced dormancy, and reduced germination speed. The differences between the Rc and Pb loci in the flavonoid type/content and the size of pleiotropic effects could partly explain the predominance of red pericarp-colored genotypes in wild and weedy rice and in pigmented specialty cultivars.