Aim: To elucidate the possible mechanism of phytoplasma elimination from periwinkle shoots caused by indole-3-butyric acid (IBA) treatment. Methods and Results: It has been shown that a transfer of in vitro-grown phytoplasma-infected Catharanthus roseus (periwinkle) plantlets from medium supplemented with 6-benzylaminopurine (BA) to one supplemented with IBA can induce remission of symptoms and even permanent elimination of 'Candidatus Phytoplasma asteris' reference strain HYDB. Endogenous auxin levels and general methylation levels in noninfected periwinkles, periwinkles infected with two 'Candidatus Phytoplasma' species and phytoplasma-recovered periwinkles were measured and compared. After the transfer from cytokinin-to auxin-containing media, healthy shoots maintained their phenotype, methylation levels and hormone concentrations. Phytoplasma infection caused a change in the endogenous indole-3-acetic acid to IBA ratio in periwinkle shoots infected with two 'Candidatus Phytoplasma' species, but general methylation was significantly changed only in shoots infected with 'Ca. P. asteris', which resulted in the only phytoplasma species eliminated from shoots after transfer to IBA-containing medium. Both phytoplasma infection and treatment with plant growth regulators influenced callose deposition in phloem tissue, concentrations of photosynthetic pigments and soluble proteins, H2O2 levels and activities of catalase (CAT) and ascorbate peroxidase (APX). Conclusion: Lower level of host genome methylation in 'Ca. P. asteris'-infected periwinkles on medium supplemented with BA was significantly elevated after IBA treatment, while IBA treatment had no effect on cytosine methylation in periwinkles infected with 'Candidatus Phytoplasma ulmi' strain EY-C. Significance and Impact of the Study: Hormone-dependent recovery is a distinct phenomenon from natural recovery. As opposed to spontaneously recovered plants in which elevated peroxide levels and differential expression of peroxide-related enzymes were observed, in hormone-dependent recovery changes in global host genome, methylation coincide with the presence/absence of phytoplasma.