DNA methylation was investigated as a possible mechanism for regulation of floral gene expression in stolbur phytoplasma-infected tomato buds. Expression of methylase and demethylase genes was found to be globally down-regulated in tomato plants infected with stolbur isolate PO, but not in those infected with isolate C. These results are consistent with the finding that SlDEF, a gene orthologous to arabidopsis APETALA3 which is involved in petal formation, was down-regulated in stolbur PO-infected buds and remained unaffected in stolbur C-infected buds, and with the fact that the two stolbur phytoplasma isolates C and PO induce distinct symptoms. Because of variations between the different cell-types of the flower buds, the DNA methylation status of SlDEF could not be clearly established. However, the finding that treatment of stolbur PO-infected plants with 5-azacytidine partially restored SlDEF gene expression strongly suggests that DNA methylation is involved in down-regulation of floral development genes in stolbur PO-infected tomatoes.