The formation of morphological boundaries between developing tissues is an integral mechanism for generating body forms and functions. For the molecular and cellular studies of how such morphological boundaries form, somitogenesis serves as a particularly good model. When an intersomitic boundary forms in the anterior end of the presomitic mesoderm, cells undergo dynamic behaviors including a separation of tissues and changes in cell shape from mesenchymal to epithelial. Moreover, these events occur repeatedly and periodically. We here overview the inductive events that have recently been shown to play important roles in the formation of the intersomitic fissures. We then discuss molecular mechanisms underlying these inductive actions, and also discuss how the fissure formation is interpreted by the subsequent morphogenesis, including cell epithelialization and the acquisition of anterior–posterior identities in the newly formed somite. Thus, somitogenesis provides a unique model to understand how sequentially occurring processes of morphogenesis are coordinated in a 3-D environment.