We isolated DEAD-box genes from three ascidian species (Ciona intestinalis, Ciona savignyi, and Halocynthia roretzi) by polymerase chain reaction methods. We obtained two types from each of C. intestinalis and C. savignyi, and four types from H. roretzi. The first type (DEAD1) belonged to the vasa subfamily, the second type (DEAD2) to the PL10 subfamily, the third type (DEAD3) to the p68 subfamily, and the forth type (DEAD4) did not belong to any of the subfamilies. We further analyzed in detail the expression pattern of C. intestinalis vasa-type gene (Ci-DEAD1) by in situ hybridization. In sections of the ovary and testis, the Ci-DEAD1-specific probe reacted intensely to small germ cells, oogonium, and/or oocyte and spermatogonium and/or spermatocyte, respectively. In whole-mount specimens of juveniles this probe specifically reacted to the primordial germ cells in the gonad rudiment. These gonad-specific expressions were confirmed by reverse transcriptase polymerase chain reaction of RNA from various tissues. The transcript was present in unfertilized eggs and in the central cytoplasm of blastomeres until the two-cell stage. During the second cleavage a part of the transcripts moved to the posterior region of embryos and, during early embryogenesis, was localized in the posterior-most blastomeres. In the tailbud, one or two hybridization signals were detected in the caudal endodermal strand. Based on these observations, we propose precursors of primordial germ cells in ascidians.