DNA methylation plays a role in plant responses to the stress and the stress-induced epimutations could be inherited over generations,helping plants adapt to the stressful environments.Upland rice has been domesticated in water limited environments and accumulated drought-induced epimutations,leading to the adaptive epigenetic divergence between it and lowland rice.In this study,epigenetic variations are investigated in 180 rice landraces under normal,osmotic,and re-watering conditions via MSAP technique.Great alterations of DNA methylation covering >50%individuallocus combinations were recorded when rice materials are treated with osmotic stress.Among these alterations,~30%are kept their status in the osmotic stress after rewatered for two days.The epigenetic differentiation between upland and lowland rice could be revealed by PCoA in which some upland and lowland rice are separated along the first coordinate.However,the adaptive divergence between upland and lowland rice mainly occurs on the highly divergent epiloci(HDE)whose ΦST is ranged from 0.134~0.187.Additionally,the ΦST of HDE between upland and lowland rice within a region is significantly correlated with the average rainfalls.The HDE prefers to occur on drought-responding genes and genes at HDE express differently between upland and lowland rice may.Our study provides evidences the DNA methylation plays an important role in rice ecotypes adapt to environments of contrasting soil-water conditions,contributing to the evolution of rice drought-resistances in upland rice.