This record contains supplementary information for the article "Genetic and epigenetic differentiation across intertidal gradients in the foundation plant Spartina alterniflora". It contains the barcodes (barcodes.txt), the reference contigs (contigs.fasta.gz), the annotation of the reference contigs (mergedAnnot.csv.gz), the SNPs (snps.vcf.gz), the methylation data (methylation.txt.gz), and the experimental design (design.txt). All data are unfiltered. All reads are available on SRA (PRJNA798549). Note that the barcode sequences and the control nucleotide were already removed from the demultiplexed files (hence, for each sample, reads are also split into "watson" and "crick" based on the control nucleotide).