Ecological genomics approaches have informed us about the structure of genetic diversity in natural populations that might underlie patterns in trait variation. However, we still know surprisingly little about the mechanisms that permit organisms to adapt to variable environmental conditions. The salt marsh foundation plant Spartina alterniflora exhibits a dramatic range in phenotype that is associated with a pronounced intertidal environmental gradient across a narrow spatial scale. Plants are taller in the low marsh habitat at the water's edge and they decline in stature as elevation increases toward the high marsh habitat. In addition to genetic differences that might underlie this phenotypic variation, non-genetic molecular level processes like DNA methylation contribute to organismal response. We used epigenotyping-by-sequencing (epiGBS) to investigate patterns of genomic and epigenomic diversity in natural S. alterniflora populations across the intertidal environmental gradient.