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The budding ascidian Polyandrocarpa misakiensis proliferates asexually by budding. The atrial epithelium is a multipotent but differentiated tissue, which transdifferentiates into various tissues and organs after the bud separates from the parental body. We isolated cDNA clones homologous to the myc proto‐oncogene from P. misakiensis. The cDNA, named Pm‐myc, encoded a polypeptide of 639 amino acid residues, containing Myc‐specific functional motifs, Myc box I and Myc box II, and the basic helix‐loop‐helix domain. Expression of Pm‐myc was observed in the atrial epithelium in the organ‐forming region of the developing bud, where the epithelial cells dedifferentiate and re‐enter the cell cycle. The expression was also observed in fibroblast‐like cells, which are known to participate in the organogenesis together with the epithelial cells. Unexpectedly, the atrial epithelium expressed Pm‐myc more than one day before the dedifferentiation. The organogenesis was disturbed by Pm‐myc‐specific double‐stranded RNA. In situ hybridization revealed that Pm‐myc‐positive fibroblast‐like cells disappeared around the organ primordium of the dsRNA‐treated bud. The results suggest that the mesenchymal‐epithelial transition of fibroblast‐like cells is important for the organogenesis in this budding ascidian species.