During embryogenesis of the ascidian Halocynthia roretzi, exactly eight-hundred epidermal cells are formed in the larva, and the lineage of the cells has been almost completely described. In the present study, we examined the spatio-temporal expression patterns of eight epidermis-specific genes which we already isolated. In situ hybridization of whole-mount specimens unambiguously demonstrated that the expression patterns of the eight genes were not identical, and that they were categorizable into several types. Transcripts of seven genes were restricted to presumptive epidermal cells, although transcripts of one gene were evident in the presumptive neural cells in addition to the presumptive epidermal cells. Therefore, most of the epidermis-specific genes in ascidian embryos are expressed in lineage-associated manner. We discuss these results in relation to the question of whether (a) epidermis-specific genes are expressed exclusively in presumptive epidermal cells prior to neural induction, or (b) the genes are first expressed in both epidermal precursors and precursors of the central nervous system, then the gene expression is downregulated in the latter after the completion of neural induction. Interestingly, cells of the anterior-most region as well as the dorsal midline of the tailbud embryo did not express most of the epidermis-specific genes, suggesting regional differences in the embryonic epidermis. Some other genes might be expressed in a complementary pattern in these regions.