A protocol for the cultivation of Larix sibirica Ledeb. by somatic embryogenesis was developed (RF Patent No. 2456344, 2012). The L. sibirica collection consisted of 22 actively proliferating cell lines (CLs) obtained from immature zygotic embryos. The age of CLs ranged from 1 to 14 years. CLs differed in their growth intensity, embryonic productivity, hormonal balance, and genetic stability, as well as in their regenerative ability. In most proliferating CLs, the formation of globular somatic embryos continued for 2–4 years. Here, a number of CLs actively proliferated for 9–14 years or more. The formation of embryogenic cultures in L. sibirica is associated with the content of phytohormones and their localization in embryo cells. The cytogenetic studies revealed the genetic stability of young CLs (up to 1 year), in which the karyotype consisted of the diploid number of chromosomes (2n = 24). Genomic mutations were observed in the long-term proliferation of CLs. Individual CLs can maintain cytogenetic stability for many years; such CLs can successfully be used to preserve germplasm, obtain planting material, and for plantation reforestation.