Somatic embryogenesis (SE) in conifers is at the base of nearly all biotechnology products that potentially might be developed including transgenic trees. SE is a powerful tool for clonal propagation that has opened avenues for deployment of superior clonally replicated planting stock in forest plantations. Although the SE process can be managed for high efficiency there are still several problems that require better understanding of underlying causes. One phenomenon, which occurs after the long-term culture of embryogenic tissue, particularly of pines, is the loss of ability to produce mature somatic embryos and consequently plants. Such unproductive cultures must be replaced, which is both expensive and undesirable. In an attempt to get an insight into the differences between young, primary lines of embryonal mass of maritime pine that produced somatic embryos and the same lines of significantly increased age that stopped producing somatic embryos, we analyzed in both types of material the levels of endogenous hormones and their metabolites, polyamines, global DNA methylation and DNA methylation patterns. DNA methylation plays an important role in regulation of gene expression and may cause epigenetic change leading to suppressed embryogenic potential. To determine if the DNA methylation could be altered, we exposed the cultures to different concentrations of hypomethylating agents such as 5-aza-2'- deoxycytidine, 5-aza-cytidine and zebularine and tested the embryogenic potential of a line after the treatment. For comparison, we induced secondary SE from a few mature somatic embryos of the same lines and carried out the same as above analyzes. Secondary SE has been implicated in restoring/enhancing the embryogenic potential of a given line and therefore theoretically the tissue was expected to be biologically similar to the primary young line. Our results indicated that embryogenic cultures of different ages varied with respect to the polyamines levels and DNA methylation pattern but not with respect to the hormone concentration. Treatment of the cultures with the hypomethylating agents resulted in different methylation patterns and somatic embryo production ability.