A hallmark of flowering plants is sexual reproduction, with the embryo a key player. In double fertilization, the zygote (fertilized egg) first establishes its apical-basal polarity within the single cell. With cell division and differentiation, the proembryo forms a apical-basal axis and develops through pattern formation and organogenesis. Recent advances have shown that the whole process of embryogenesis is regulated by auxin at levels of biosynthesis, polar transport and signal transduction. In this review, we highlight our current understanding, mainly from studies in Arabidopsis, of the molecular mechanisms by which auxin controls embryogenesis. These mechanisms include the establishment of polarity of zygotes, apical-basal axis of embryos, differentiation of protoderm, transition of radial symmetry to bilateral symmetry, formation of hypophysis, shoot apical meristem and root apical meristem. In addition, we briefly introduce the embryogenesis process not regulated by auxin.