Adventitious organogenesis from zygotic embryos is one of the most reliable techniques to propagate clonal Pinus radiata individuals. Regulation of gene expression has an important role to generate a correct caulogenic pattern, and genomic DNA methylation is amongst the main studied regulatory mechanisms in animals and plants. The aim of this work is to evaluate the role of DNA methylation and histone H4 acetylation during different cell reprogramming processes. Embryo macromorphological responses to each growth regulator were correlated to DNA methylation and acetylated H4 histone content over time. Immunodetection of 5-mdC and AcH4 in whole embryos revealed differences in the tissue depending on the growth regulator. Adventitious shoot induction by benzyladenine is associated with a DNA hypomethylation. The distribution along the tissue of the methylation signal suggests a possible inhibition of growth and elongation in the embryos. However, a hypomethylation in the cotyledons during adventitious shoot induction could indicate an active gene expression during the organogenic process. On the other hand, alteration of embryo growth induced by indole butyric acid and 2,4-dichlorophenoxyacetic acid occurs along a wide change in DNA methylation and H4 histone acetylation content and distribution. These results show that the action of the different growth regulators is epigenetically regulated in both apical meristems.