Somatic embryogenesis in Cyclamen persicum was first reported in 1984 and has potential applications for propagation and breeding of this economically important ornamental crop. This in vitro regeneration system can be used for vegetative propagation of parental lines of F1 hybrids and elite plants, production of artificial seeds, Agrobacterium tumefaciens-mediated genetic transformation, long-term cryopreservation, protoplast to plant regeneration and somatic hybridization. Somatic embryogenesis was shown to be a powerful propagation system for some C. persicum genotypes, but commercial application in large scale so far is hindered by several limitations, i.e., asynchronous development, malformations or secondary somatic embryogenesis. However, recent molecular approaches by transcriptomic and proteomic analyses were undertaken in order to better understand and control this in vitro regeneration system and to overcome these problems. Our studies aim at comparing somatic embryos to their zygotic counterparts regarding their proteomes. Protein separation by two dimensional isoelectric focusing - sodium do-decyl sulfate polyacrylamide gel electrophoresis led to a resolution of about 1000 protein spots per gel, of which the first 253 were identified by mass spectrometry. Most were found to be involved in glycolysis/gluconeogenesis and stress response pathways. A proteome reference map of zygotic embryos will be publicly released soon and may serve as a basis for further investigations and improvements of somatic embryogenesis.