Studies were undertaken to identify the basis of differences in seed coat pigmentation between selected yellow- and brown-seeded Brassicaceae, and near-isogenic yellow- and brown-seeded lines of </i>Brassica carinata</i> (PGRC/E 21164). Histochemical analyses of dissected seed coats from six genera of the Brassicaceae revealed condensed tannin (proanthocyanidin) and phlobaphene pigments in dark-seeded species and in scattered spots in most yellow-seeded species. Anthoeyanins were not detected in any seed coat tissue of these species. In leaf tissue, anthocyanin content was lower in yellow-seeded 'B. carinata' at the three- to four-leaf stage grown at 20 to 25°C, compared to similarly grown brown-seeded plants. At 15 to 18°C, both yellow- and brown-seeded lines produced similar amounts of anthocyanin in the seedling leaves. In TLC and HPLC analyses, 't'-cinnamic acid, dihydromyricetin [trace amounts], dihydroquercetin, dihydrokaempferol and flavonols (quercetin, kaempferol) were more abundant in extracts from seed coats of yellow-seeded ' B. carinata' than in extracts from seed coats of brown-seeded ' B. carinata'. Myricetin was not detected in any seed coat extracts. Mass spectra were determined for phenylpropanoid and flavonoid aglycones from the seed coat extracts and for authentic standards. Dihydroflavanol reductase ('DFR') transcripts from developing seed were absent or less abundant at 5, 10, 20 and 30 days after pollination in the yellow-seeded line compared to the brown-seeded line of 'B. carinata'. 'DFR' transcripts in seedling leaves from the yellow-seeded line grown in warm, bright conditions were less abundant compared to similarly grown brown-seeded material. Seedlings grown at 15 to 18°C produced greater amounts of 'DFR' transcript in both yellow- and brown-seeded lines of 'B. carinata' compared to warm-grown plants. Data from these experiments suggest that seed coat pigmentation in the Brassicaceae is due to condensed tannin and phlobaphene accumulation, not anthocyanins, and that seed coat pigment biosynthesis is down-regulated at dihydroflavonol reductase. The regulatory factor controlling 'DFR' expression in developing seed may be temperature sensitive and also affect anthocyanin biosynthesis in seedlings and in related metabolic pathways: thioglycolic lignin concentration was significantly lower in the yellow-seeded Brassicaccae and in the seed coat tissue of yellow-seeded 'B. carinata' compared to dark-seeded samples.