Clonal propagation of Quercus suber via somatic embryogenesis is an alternative to conventional tree propagation methods; however, complete maturation of somatic embryos is considered the major bottleneck for mass propagation of Quercus species. During somatic embryogenesis, embryo development and maturation are controlled by signaling pathways that integrate information from genetic and epigenetic programs as well as hormonal signals. Therefore, in this study genes were identified related to epigenetic regulation and the abscisic acid (ABA) pathway during development and maturation of cork oak somatic embryos. A total of eight expressed sequence tags were obtained of genes encoding a 9-cis-epoxycarotenoid dioxygenase (NCED), two histone deacetylases (HDA6 and HDA19), two histone monoubiquitinases (HUB1 and HUB2), a histone H3 kinase (AUR3) as well as genes related to chromatin remodeling processes PICKLE and VP1/ABSCISIC ACID INSENSITIVE 3-LIKE 1 (VAL1). The analysis of the expression patterns of selected genes during different developmental stages indicated that QsNCED3 may play a role in ABA synthesis during embryogenesis. The change in the expression levels for all seven genes associated with epigenetic regulation showed that QsHUB1 and QsHUB2 may have a role in ABA signalling while QsHDA6 and QsHDA19 could act in different pathways than in Arabidopsis. Furthermore, expression levels of QsAUR3 indicated that histone phosphorylation is an early epigenetic mark in Q. suber somatic embryos while QsPICKLE and QsVAL1 may be necessary for the correct development of cork oak somatic embryos.