Comprehensive proteomic characterizations were performed aiming to create proteome reference maps for somatic and zygotic embryos of Cyclamen persicum. Separation by two dimensional isoelectric focusing - sodium dodecyl sulfate polyacrylamide gel electrophoresis led to a resolution of more than 800 protein spots for each tissue. Approximately 70% of the spots likewise appeared in both zygotic and in somatic embryo's protein fractions. However, differential gel electrophoresis analyses revealed pronounced differences in abundances for the majority of proteins present in both tissues. MS analyses for 300 reproducible spots in total (263 of the zygotic embryos' protein fraction and 37 spots appearing specifically in the somatic embryos' proteome) led to identification of 261 proteins, 35 of which were specific or highly abundant in gels of the somatic embryo's tissue. Most identified proteins were found to be involved in glycolysis or gluconeogenesis and stress response pathways.