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DNA methylation plays an important role in plant development and response to multiple environmental stresses that cause a DNA methylation variation and likely persist in the process of gene expressions. In this study, we report an effect of salt stress (SS) at a 9:1 ratio of NaCl to Na2SO4 as well as alkali stress (AS) at a 9:1 ratio of NaHCO3 to Na2CO3 in sunflower on the DNA methylation. The results showed the DNA methylation at CG locations in sunflower leaves was much higher than that in roots, but more variations of the DNA methylation occurred in roots under two stresses, especially the alkali one. In addition, qRT-PCR validations further revealed significant changes in the gene expression pertaining to the DNA methylations, especially in roots. We hypothesized that roots were the first plant parts to be in contact with various abiotic stresses from the surrounding soil, sent out the stress signals throughout the whole plant, and then make adaptive responses quickly. Our findings from this study have provided some evidence that DNA methylation might be directly involved the signal generation and transmission in roots, which modifies DNAs and regulates the signally more extensively and sophisticatedly in roots than those in leaves. The intensified mechanism and regulation of DNA methylation in sunflower roots are very much involved in plant alkali tolerance and deserve a further investigation thoroughly.