Cell lineage analysis of the ascidian Halocynthia roretzi demonstrated that a pair of cells situated on the right and left sides of 64-cell stage embryos, termed the A7.6 cells, give rise to trunk lateral cells (TLCs) of the tadpole larva and that after metamorphosis TLCs give rise to various mesodermal tissues of the adult, in particular all of the blood cells or coelomic cells. Here we report the isolation and characterization of cDNA clones for two TLC-specific genes HrTLC1 and HrTLC2. HrTLC1 encodes for a novel protein while HrTLC2 encodes for a polypeptide with RNA recognition motifs. Zygotic expression of HrTLC1 and HrTLC2 begins at the neural plate stage and transcripts of both these genes are restricted to TLCs.