Embryo development is a very key phase in the life cycle of seed plants. At maturity, the embryo contains the complete machinery to elaborate the entire plant body. While the embryogenic process is an innate feature of the zygote, gametic and somatic cells can undergo embryogenesis under the appropriate culture conditions. Embryogenesis is a highly regulated process and the use of mutants, especially in Arabidopsis, has allowed the identification of genes regulating pattern formation during this process. The use of such mutants has revealed the critical roles of auxin levels and transport in the establishment of embryo axis. Root and shoot apical meristem function and integrity have been defined by examination of genes involved in their identity and function. Further knowledge of the molecular and biochemical aspects of zygotic embryogenesis should contribute to our understanding of the underlying regulatory pathways and networks and also provide critical insights into unique totipotent features of the plant cell.