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Background: Several studies showed genome-wide DNA methylation during Arabidopsis embryogenesis and germination. Although it has been known that the change of DNA methylation mainly occurs at CHH context mediated by small RNA-directed DNA methylation pathway during seed ripening and germination, the causality of the methylation difference exhibited in natural Arabidopsis ecotypes has not been thoroughly studied. Results: In this study we compared DNA methylation difference using comparative pairwise multi-omics dynamics in Columbia-0 (Col) and Cape Verde Island (Cvi) ecotypes. Arabidopsis genome was divided into two regions, common regions in both ecotypes and Col-specific regions, depending on the reads mapping of whole genome bisulfite sequencing libraries from both ecotypes. Ecotype comparison was conducted within common regions and the levels of DNA methylation on common regions and Col-specific regions were also compared. we confirmed transcriptome were relatively dynamic in stage-wise whereas the DNA methylome and small RNAome were more ecotype-dependent. While the global CG methylation remains steady during maturation and germination, we found genic CG methylation differs the most between the two accessions. We also found that ecotype-specific differentially methylated regions (eDMR) are positively correlated with ecotype-specifically expressed 24-nt small RNA clusters. In addition, we discovered that Col-specific regions enriched with transposable elements (TEs) and structural variants that tend to become hypermethylated, and TEs in Col-specific regions were longer in size, more pericentromeric, and more hypermethylated than those in the common regions. Through the analysis of RdDM machinery mutants, we confirmed methylation on Col-specific region as well as on eDMRs in common region are contributed by RdDM pathway. Lastly, we demonstrated that highly variable sequences between ecotypes (HOT regions) were also affected by RdDM-mediated regulation. Conclusions: Through ecotype comparison, we revealed differences and similarities of their transcriptome, methylome and small RNAome both in global and local regions. We validated the contribution of RdDM causing differential methylation of common regions. Hypermethylated ecotype-specific regions contributed by RNA-directed DNA methylation pathway largely depend on the presence of TEs and copy-gain structural variations. These ecotype-specific regions are frequently associated with HOT regions, providing evolutionary insights into the epigenome dynamics within a species. [ABSTRACT FROM AUTHOR]