What pigment causes the red color in cotton leaves? The main pigment associated with red colored leaves in cotton is anthocyanin. This pigment is the same compound which produces the red color noted in deciduous forests in the fall before they shed their leaves.

The synthesis of anthocyanin, the pigment which typically causes the reddening, is commonly increased after leaves are exposed to light following multiple abiotic and biotic stresses. Subsequently, anthocyanin may become visible at multiple times through the growing season.