Abstract It is not known whether exposure to persistent organic pollutants (POPs) cause epigenetic changes in marine mammals. Ringed seals are a key species at the higher trophic levels of arctic marine ecosystems, and may be particularly vulnerable due to bio-magnification of POPs in the food web. DNA methylation is a well-studied epigenetic mechanism, and is important for gene regulation and chromosomal stability. Changes in DNA methylation may lead to diseases such as cancer and developmental disruption. The aims of this study are (i) to investigate whether sex, age and moulting status affect global DNA methylation measured as percent 5-methylcytosine (%5-mC) in tissues of ringed seals, (ii) to compare %5-mC levels in liver and kidney of ringed seals, (iii) investigate whether %5-mC differs in tissues of ringed seals from two differently polluted areas, Svalbard and the Baltic Sea, and (iiii) clarify whether there are associations between individual POPs and %5-mC in ringed seal liver and kidney from Svalbard and the Baltic Sea. ELISA was applied to measure %5-mC. POPs were measured from liver and plasma by gas chromatography- mass spectrophometry (GC-MS). Univariate analysis were used for investigation of %5-mC in relation to biological factors and area, while principal components analysis (PCA) and non-parametric correlation analysis was used to investigate the relationship between %5-mC and POPs. A significant difference in %5-mC was found between moulting and pre-moulting individuals, and between liver and kidney. Sex, age and area did not affect %5-mC. Several PCBs, PBDEs, CHLs, p,p -DDE and 4'-OH-CB172 were significantly correlated with %5-mC, but the results were not the same between areas or tissues. Correlations between POPs and %5-mC were negative in liver and kidney from Svalbard, and in kidney from the Baltic Sea, while positive in liver from the Baltic ringed seals. The results indicated lower %5-mC levels in moulting seals compared to pre-moulting which could be caused by a reduction in dietary methyl donors due to fasting, leading to depletion of methyl donors in the cells. However, precaution must be taken due to small sample size. The lower %5-mC levels found in liver compared to kidney may be caused by a depletion of methyl-donors in hepatic cells as a result of enhanced xenobiotic metabolism and oxidative stress induced by POP exposure, in addition to reduced intake of dietary methyl-donors. Interaction by other contaminants than those measured here, mixture toxicity and non-linear relationships might also play a role in the relationship between %5-mC and POPs.