Salinity can negatively impact crop growth and yield. Changes in DNA methylation are known to occur when plants are challenged by stress and have been associated to the regulation of stress-response genes. However, the role of DNA-methylation in moderating gene expression in response to salt stress has been relatively poorly studied among crops such as barley. Here we assess the extent of salt-induced alterations of DNA methylation in barley, and their putative role in perturbed gene expression. Using Next Generation Sequencing, we screened the leaf and root methylomes of five divergent barley varieties grown under control and three salt concentrations, to seek genotype independent salt-induced changes in DNA methylation. Salt stress caused increased methylation in leaves but diminished methylation in roots with a higher number of changes in leaves than in roots, indicating that salt induced changes to global methylation are tissue specific. DMMs were mostly located in close proximity to repeat elements but also 1094 genes, of which many possessed GO terms associated with plant responses to stress. Identified markers identified have potential value as sentinels of salt stress and provide a start point to understand the functional role of DNA methylation in facilitating barley’s response to this stressor.