The forestry industry has integrated somatic embryogenesis into its clonal programs due to the generation of a high number of plants from selected genotypes at low cost. Somatic embryos are generated in a stressful environment after multiplication of the proembryogenic masses; thus, it is critical to determine the degree of stability of the embryogenic cultures and their potential for mass propagation. Maturation ability in cultures of different ages was evaluated in conjunction with the integrity of the proembryogenic masses, germination rate, hypocotyl and root length, plant conversion, and ex vitro survival. To identify differences in embryogenic tissue from different subcultures, their DNA was analyzed using FT-IR spectroscopy. A significant decrease in the production of somatic embryos was detected from week 15, and some lines even stopped producing embryos. Germination rate, hypocotyl length, and plant conversion were negatively affected by long-term cultivation, while root length and ex vitro survival were not significantly affected. The results obtained from the FT-IR spectroscopy analysis indicate that it is feasible to use mid-infrared spectroscopy to differentiate between embryogenic tissues with different cumulative subculture times based on the spectra obtained from their DNA, which is directly related to maturation ability.