Previous studies showed that chalcone synthase (chs) silencing in flax (Linum usitatisimum) induces a signal transduction cascade that leads to extensive modification of plant metabolism. Result presented in the current study, performed on field grown flax plants - (across the whole vegetation period) demonstrates that, in addition to its role in tannin and lignin biosynthesis, the chs gene also participates in the regulation of flavone biosynthesis during plant growth. Apigenin and luteolin glycosides constitute the flavones, the major group of flavonoids in flax. Alterations in their levels correlate with plant growth, peaking at the flower initiation stage. Suppression of chs gene expression causes significant changes in the ratio of flavone constituents at the early stage of flax growth. A significant correlation between flavonoid 3'-hydroxylase (F3'H) gene expression and accumulation of luteolin glycosides has been found, indicating that flavone biosynthesis during flax growth and development is regulated by temporal expression of this gene. The lack of such a correlation between the flavone synthase (FNS) gene and flavone accumulation in the course of plant growth suggests that the main route of flavone biosynthesis is mediated by eriodictyol. This is the first report indicating the ratio of flavone constituents as a potent marker of flax growth stages and temporal expression of F3'H, the key gene of their biosynthesis.