In germline cells of early C. elegans and Drosophila embryos, repression of zygotic gene expression appears to be essential to maintain the germ cell fate. In these animals, specific residues in the carboxy-terminal domain (CTD) of RNA polymerase II large subunit (RNAP II LS) are dephosphorylated in the germline cells, whereas they are phosphorylated in the somatic cells. We investigated, in early embryos of the ascidian Halocynthia roretzi, the expression patterns of three genes that are essentially expressed in the entire embryo after the 32-cell stage. We found that the expression of these genes was inactive in the putative germline cells during the cleavage stages. Once cells were separated from the germline lineage by cleavages, the expression of the genes was initiated in the cells. These results suggest that repression of transcription in germline cells may also be common in chordate embryos. We then examined the phosphorylation state of the CTD of RNAP II using a phosphoepitope-specific antibody. At cleavage stages after the 32-cell stage, CTD was phosphorylated in every blastomere, including the germline cells. Therefore, in the ascidian, the inactivation of zygotic transcription is not correlated with dephosphorylation of the CTD. These observations indicate that zygotic transcription is inactivated in ascidian germline cells, but the mechanism of the repression may differ from that in C. elegans and Drosophila.