Stokes aster [Stokesia laevis (J. Hill) Greene] is a herbaceous perennial endemic to the coastal plains of the southeastern United States. Anthocyanin and copigment aglycones from flowers were characterized using high-performance liquid chromatography. Blue, lavender, violet, and albescent flowers each contained the anthocyanidin petunidin, although albescent flowers contained a substantially smaller amount. Pale pink flowers were found to contain only cyanidin. Anthocyanins and carotenoids were not present in pale yellow flowers of this species. All flowers contained the flavone luteolin. Genetic analysis of F1, F2, and BC1 populations suggested that flower color in stokes aster is controlled by at least three loci. F2 populations of blue × albescent and blue × pale yellow flowering plants segregated in a 3:1 ratio of blue to albescent or pale yellow flowered progeny, indicating that albescent and pale yellow flower colors were recessive and each controlled by a single locus with two alleles. BC1 populations supported these results. We propose the symbols A and Y: AA and YY plants synthesize a normal amount of anthocyanins, aa plants synthesize a reduced amount of anthocyanins, and yy plants do not synthesize anthocyanins. When the two mutant phenotypes (i.e., albescent [aa] and pale yellow [yy]) were crossed, the F1s were blue, and the F2 segregated in a 9 blue:3 albescent:4 yellow ratio, indicating that the recessive locus (y), when homozygous, was epistatic to other loci involved in anthocyanin production (e.g., A), and that the genotypes of the parents used in these crosses were aaYY (albescent) and AAyy (pale yellow). F1, F2, and BC1 populations of blue (petunidin) × pale pink (cyanidin) flowering plants revealed that cyanidin production was recessive and controlled by a single locus, P, with two alleles, whereby PP plants synthesize petunidin and pp plants synthesize cyanidin. It was difficult to distinguish albescent- and pale pink-flowered progeny in segregating generations, therefore three genetic models were proposed and tested to determine the genotype(s) (i.e., AApp, Aapp, or aapp) of the pale pink-flowered plants. Based on these analyses, we propose a theoretical biochemical pathway for flavonoid biosynthesis in stokes aster.