Ascidian is a useful experimental animal for studying body planning principles and host defense mechanisms employed by the phylum chordata. Toward this goal, genome and cDNA/EST projects of Ciona intestinalis have been undertaken. Using cDNAs and ESTs derived from Ciona hemocytes, we identified 79 possible hemocyte-preferential transcripts and determined the cDNA sequence of each clone. The amino acid sequence of each encoded polypeptide was predicted as well. Among these cDNAs, we identified three transcripts that may be involved in characteristic cell-cell communication in Ciona. These transcripts encoded leucine-rich repeat-containing RP105-like, IL-17 receptor/similar expression to FGF-like, and ectodysplasin-like polypeptide of the tunmr necrosis factor famlly, and they are expressed abundantly in hemocytes.