Forest trees are complex organisms which nowadays are facing threats under climate change, diseases, insects and pathogens. Their ability to adapt to changing environments depends on their genetic and epigenetic integrity and the relationship between them. The term epigenetics refers to the study of heritable changes in gene expression and function that cannot be explained by changes in DNA sequence. The study of epigenome, at the landscape level may add important acumen in order to identify genomic regions which are associated with adaptive variation. Although population genetic analysis revealed how genetic diversity, structure and linkage can be implemented the significance of variation in epigenetic processes at the population level reveals a composite challenge which remains undetermined. That difference is associated with the inability to associate epialleles with phenotypic variance, whereas for classic genetic analysis, genetic variation can explain a percentage of phenotypic variation. This complex issue has recently become a priority and studies which target genetic and epigenetic diversity were conducted in natural forest tree populations in order to identify the relationship between them and examine additional component of epigenetic diversity in phenotypic variance and plasticity. By estimating epigenetic diversity and especially DNA methylation, improvement of our understanding of the mechanisms underlying natural variation in ecologically important traits will be accomplished. A mini review will be presented in order to enhance our understanding for epigenetic mechanisms in forest tree populations.