Flax (Linum usitatissimum L.) is an important crop used in various industries. Fusarium oxysporum is the causative agent of Fusarium wilt, and this disease is the most harmful for flax. The most effective way to control this pathogen is to develop resistant varieties. The mechanisms of flax resistance to F. oxysporum are still unclear. In our work, we analyzed the data obtained by transcriptome sequencing of resistant and susceptible flax varieties grown under control conditions and after inoculation with F. oxysporum . We evaluated expression alterations of CCR , CCoAOMT , COMT , and 4CL gene families, which are involved in lignin biosynthesis, and revealed their significant upregulation in flax varieties in response to F. oxysporum .