Abstract In this work, we attempted to elucidate mechanisms of flax fiber biogenesis by measuring, using qPCR, expression of the cellwall related genes (cellulose synthase, cellulose synthase-like and chitinase-like genes) in stems of two contrasting fiber quality subspecies of flax (Linum usitatissimum L.). We studied elongatum Vav. et Ell. (cultivar Blakit, Belarus) and crepitans Boenn. (dehiscent flax) subspecies, which are differed in the height of plants, width of stems etc. Amongst all measured genes chitinase- like Ctl19 and Ctl21 genes showed drastic difference in expression between stems of the two flax varieties, showing higher expression level in the fiber flax versus the dehiscent flax. In contrast, cellulose synthase-like CslG4 gene had lower expression levels in the stem of fiber flax than in dehiscent flax. We suggest that hemicellulose composition and cellulose - non-cellulose glycan organisation can vary between stalk cells of different flax subspecies.