Spartina alterniflora, marsh grass, is a vegetative apomicticly-reproducing halophyte native to marshes along the east coast of the United States and invasive across the world. S. alterniflora provides many ecosystem services including, but not limited to, water filtration, habitats for invertebrates, and sediment retention. Widespread diebacks of longstanding marsh grass colonies launched extensive investigations into probable mechanisms leading to patchy diebacks. There is still current debate as to the causes of a marsh dieback but environmental stress is acknowledged as a constant. Spatial epigenetic variation could contribute to variation of stress susceptibility, but the scale and structure of epigenetic variation is unknown. The current study investigates patterns of epigenetic variation in a natural population of S. alterniflora. This study examines variation of global DNA methylation within and among clones of the marsh grass Spartina alterniflora using an ELISA-like microplate reaction and observed significant heterogeneity of global DNA methylation within and among clones of S. alterniflora across the North Inlet basin, as well as significant differences of global methylation between adults and sexually produced seedlings. The present study also characterized differences for plants in a section of the population that experienced an acute marsh dieback in the year 2001 and have subsequently recolonized, finding a significant positive correlation between cytosine methylation and time period of colonization. The significant heterogeneity of global DNA methylation both within and among clones observed within this natural population of S. alterniflora and potential impacts from hypersaline environments at North Inlet suggests the need for more in-depth epigenetic studies to fully understand DNA methylation within an ecological context. Future studies should consider the effects of varying saline conditions on both global DNA and gene specific methylation.