Concomitant with the transition from the presomitic mesoderm (PSM) to somites, the periodical gene expression characteristic of the PSM is drastically changed and translated into the segmental structure. However, the molecular mechanism underlying this transition has remained obscure. Here, we show that ripply1, encoding a nuclear protein associated with the transcriptional corepressor Groucho, is required for this transition. Zebrafish ripply1 is expressed in the anterior PSM and in several newly formed somites. Ripply1 represses mesp-b expression in the PSM through a Groucho-interacting motif. In ripply1-deficient embryos, somite boundaries do not form, the characteristic gene expression in the PSM is not properly terminated, and the initially established rostrocaudal polarity in the segmental unit is not maintained, whereas paraxial mesoderm cells become differentiated. Thus, ripply1 plays dual roles in the transition from the PSM to somites: termination of the segmentation program in the PSM and maintenance of the rostrocaudal polarity.