Somatic embryogenesis is widely used in plant biotechnology, but regulatory networks underlying this process are not fully understood. This process is regulated by many protein and hormonal factors, among which WUSCHEL-related homeobox proteins are believed to play key roles. In this study, we aimed to identify the role of Medicago truncatula WOX9-1 (MtWOX9-1), an Arabidopsis thaliana WOX9 (STIMPY) homolog, in somatic embryogenesis. We demonstrated that the MtWOX9-1 promoter is active in somatic embryos, and overexpression of MtWOX9-1 leads to the increase in embryogenic capacity, as well as to the changes in expression levels of two MADS-box genes (AGL15 and AGL8 homologs), associated with embryogenesis. The data obtained suggest that stimulation of MtWOX9-1 expression may have positive impact on plant biotechnology in improving the transformation and regeneration capacity of recalcitrant plants.