During embryogenesis, the basic body plan of an organism develops from a unicellular zygote. In most flowering plants, the polar zygote divides asymmetrically, making visible the apical–basal axis in the early embryo. The molecular mechanisms governing how the zygote polarizes and how this polarity is linked to embryo axis formation have been obscure, mainly owing to the difficulties to access the zygote that is deeply embedded in the maternal tissue. In this review, we summarize recent findings identifying key regulators in Arabidopsis and developing novel approaches in various plant species, which altogether set the stage for unraveling embryo axis formation.