Technical Abstract: Chlorophylls, carotenoids, flavonoids and betalains contribute to color in economically important vegetables, fruits and floral crops. The flavonoids can be subdivided into anthocyanins and co-pigments. Color attributed to anthocyanins contributes to product sensory quality attributes, potential nutritive value, and plant stress response. The many hues observed can be attributed to a number of biochemical factors, inclusive of pigment concentration, pigment combinations and their ratios, and vacuolar pH. Shades of violet to black pigmentation in Capsicum are attributed to anthocyanin accumulation. Violet pigmentation in pepper fruit was attributed to delphinidin accumulation, whereas high concentrations of delphinidin in combination with chlorophyll accounted for black pigmentation. Anthocyanins are synthesized in response to numerous environmental factors including temperature and light stress and pathogen attack. Capsicum line ‘02C27’ accumulates anthocyanin in various tissues and accumulation is markedly sensitive to environmental stress. Real-time PCR analysis of tissues that varied in pigmentation intensity due to varying anthocyanin concentration revealed functional but differentially expressed structural genes in the anthocyanin biosynthetic pathway. Likewise, analysis of transcription factor encoding genes demonstrated differential expression of these regulatory elements, coincident with anthocyanin accumulation, in response to environmental conditions and pathogen infection.