Comparative analysis of WOX and PIN genes expression in the ovules and during somatic embryogenesis in Medicago truncatula was performed. It was shown that some WOX and PIN genes with high expression level in ovules (MtWOX11-like, STENOFOLIA, MTR_2g015000, and MtPIN10) were also activated during somatic embryogenesis. In contrast, WOX and PIN genes with low expression level in ovules didn’t demonstrate activation associated with somatic embryogenesis. These data allow to suppose that early stages of somatic and zygotic embryogenesis could be controlled by the same regulatory mechanisms.