Background: DNA methylation has been regarded as essential epigenetic mechanism involved in gene expression in specific spatiotemporal pattern.Genome-wide CpG islands (CGIs) and gene promoter regions methylation profiles have been described in numbers of tissues and cells among different species.However, the inter-tissues and inter-species DNA methylation pattern and function in other genome regions are not yet clear.To this end, we systematically analyzed the methylation difference in genome-wide CpG-sites location within seven genome categories (Up2kb, 5-UTR, CodingExon, Intron, 3-UTR, Down2kb and Intergenic regions) across multiple tissues in human and mouse.Methods: We collected methylation data in the human and mouse ES cells, B cells, fibroblast, brain, liver and lung samples detected by RRBS provided by Meissner Aet al.QDMR, a bioinformatic tool based on Shannon entropy, was utilized to quantify and identify methylation differences across these tissues and cells in both species.Further, we analyzed the functions of genes related with methylation differences within seven genome region categories by functional annotation tools in the DAVID Bioinformatics Resources 6.7 website.Results: We found that most CpG-sites located in CGIs, Up2kb, 5-UTR and Intron regions in the both species are hypomethylated.The Person Correlation Coefficient (PCC) analysis exhibited that genome-wild DNA methylation profile is significantly conserved across 6 different tissues and cells from the same species (0.806