We established a genomics based methodology to study epigenetic variation in wild plant populations by screening changes in DNA methylation (an epigenetic modification) at single-base resolution. As a study case, I'll show trends in DNA methylation variation between populations of two congeneric plants from Sierra de Cazorla with marked life history differences. In addition, we study how changes in DNA methylation would affect plant interactions through the treatment with the DNA-demethylating agent 5-azacitidine. I'll show how experimental demethylation affects both transcriptome and phenotype in the herb Erodium cicutarium (Geraniaceae), and foreshadow future experimental settings that incorporate this methodology to test its effect on plant interactions.