Anthocyanins contribute to color development in economically important vegetables, fruits and floral crops. Their expression is critical to product sensory quality attributes, potential nutritive value, and stress response. Anthocyanins are synthesized in response to numerous environmental factors including temperature and light stress and pathogen attack. We have developed several Capsicum lines, including `02C27', expressing anthocyanin pigmentation differentially in various tissues (leaf, stem, fruit and flower). HPLC analysis demonstrated that the anthocyanins within the fruit, flower and leaves of Capsicum `02C27' were identical and that the major anthocyanidin was a delphinidin glycoside. Line `02C27' exhibits anthocyanin foliar pigmentation that is accumulated differentially in response to temperature stress. Under unfavorable low temperature (20 °C day/18 °C night), mature Capsicum leaves contained 4.6 times less anthocyanin per gram fresh weight than under high (30 °C day/28 °C; day/night) temperatures. Besides containing less anthocyanin in mature leaves, young immature leaves did not develop color as quickly under the lower temperature. Utilizing cloned and sequenced gene fragments of pepper chalcone synthase (CHS), dihydroflavonol 4-reductase (DFR), and anthocyanidin synthase (ANS), we evaluated the role of transcription in regulation of flavonol biosynthesis. Analysis of anthocyanin composition and gene expression data indicated that the block in anthocyanin formation in less pigmented leaves occurred at anthocyanin synthase. In contrast to wild tupe plants, this mutant also exhibited reduced flowering and failed to set fruit under high temperature, long day conditions.