This vcf file is generated from genomic data of three-spined sticklebacks from Kiel (KIE), Germany and Nynäshamn (NYN), Sweden.The individuals from Kiel are S3, S4, S19, S20, S33, S34, S47, S48, S49, S50, S63, S64, S77, S78, S89, S90.The individuals from NYN are S5, S6, S21, S22, S35, S36, S37, S38, S51, S52, S65, S66, S79, S80, S85, S86. It contains high quality biallelic positions (GQ=20) and is filtered for minor allele frequencies of maf = 0.05, allows 40 % of missing data (13 individuals) and a read depth of >=5.Further this vcf file is subset to the inducible differentially methylated sites (DMS) (198sites) in decreasing PSU (_6PSU) with 5 kilobases (kb) before and after DMS. With this file further calculations were performed to estimate the genetic differentiation (i.e. Fst) between the different populations (see manuscript indicated below).