In humans, DNA methylation marks inherited from sperm and egg are largely erased immediately following conception, prior to construction of the embryonic methylome. Exploiting a natural experiment of cyclical seasonal variation including changes in diet and nutritional status in rural Gambia, we replicated 125 loci with a common season-of- conception methylation signature in two independent child cohorts, providing evidence of environmental effects on DNA methylation in the early embryo that persist at least until mid-childhood. Bioinformatic analysis revealed that these loci were highly enriched for metastable epialleles, parent-of-origin specific methylation and regions hypomethylated in sperm, and for H3K9me3 and H3K27me3 histone marks in multiple tissues. They tended to co-locate with endogenous retroviral (ERV1, ERVK) elements. Identified loci were influenced but not determined by measured genetic variation, notably through gene- environment interactions. To the extent that early methylation changes impact gene expression, environmental sensitivity during early embryo genomic remethylation could thus constitute a sense-record-adapt mechanism linking early environment to later phenotype.### Competing Interest StatementThe authors have declared no competing interest.

Environmentally sensitive hotspots in the methylome of the early human embryo