The shoot apical meristem (SAM) is essential for organ formation in higher plants. How the SAM is formed during plant development is poorly understood, however. In this review, we focus on several recent studies that provide new insights into the mechanism of SAM formation during embryogenesis. Recently, positive and negative regulators of the class I KNOX genes, which are thought to be necessary for SAM formation, have been identified; the Arabidopsis CUP-SHAPED COTYLEDON ( CUC) genes are required for the expression of a class I KNOX gene, SHOOT MERISSTEMLES( STM) during embryogenesis, and the Arabidopsis ASYMMETRIC LEAVES1 ( AS1), AS2, and several other genes negatively regulate KNOX gene expression in cotyledon primordia. Also, several genes that are involved in the formation of the adaxial-abaxial axis of cotyledons seem to regulate embryonic SAM formation.