Embryogenesis is a brief but potentially critical phase in the life cycle of a tree for adaptive phenotypic plasticity. Using somatic embryogenesis in maritime pine (Pinus pinaster Ait.), we found that temperature during the maturation phase affects embryo development and postembryonic tree growth for up to 3 yr. We examined whether this somatic stress memory could stem from temperature- and/or development-induced changes in DNA methylation. For this, we developed a 200 mb custom sequence capture bisulfite analysis of genes and promoters to identify differentially methylated cytosines (DMCs) between temperature treatments (18, 23, and 28 °C) and developmental stages (immature and cotyledonary embryos, shoot apical meristem of 2-yr-old plants) and investigate if these differences can be mitotically transmitted from embryonic to postembryonic development (epigenetic memory). We revealed a high prevalence of temperature-induced DMCs in genes (8% to 14%) compared to promoters (<1%) in all 3 cytosine contexts. Developmental DMCs showed a comparable pattern but only in the CG context and with a strong trend toward hypomethylation, particularly in the promoters. A high percentage of DMCs induced by developmental transitions were found memorized in genes (up to 45%–50%) and promoters (up to 90%). By contrast, temperature-induced memory was lower and confined to genes after both embryonic (up to 14%) and postembryonic development (up to 8%). Using stringent criteria, we identified 10 genes involved in defense responses and adaptation, embryo development, and chromatin regulation that are candidates for the establishment of a persistent epigenetic memory of temperature sensed during embryo maturation in maritime pine. Here, we provide evidence that DNA methylation marks established during the embryonic phase are transmitted to the postembryonic plant development phase.