Abstract The tunicates form a group of filter-feeding marine animals closely related to vertebrates. They share with them a number of features such as a notochord and a dorsal neural tube in the tadpole larvae of ascidians, one of the three groups that make tunicates. However, a number of typical chordate characters have been lost in different branches of tunicates, a diverse and fast-evolving phylum. Consequently, the tunic, a sort of exoskeleton made of extracellular material including cellulose secreted by the epidermis, is the unifying character defining the tunicate phylum. In the larva of ascidians, the tunic differenBates in the tail into a median fin (with dorsal and ventral extended blades) and a caudal fin. Here we have performed experiments in the ascidian Phallusia mammillata to address the molecular control of tunic 3D morphogenesis. We have demonstrated that the tail epidermis medio-lateral paaerning essenBal for peripheral nervous system specificaBon also controls tunic elongaBon into fins. More specifically, when tail epidermis midline idenBty was abolished by BMP signaling inhibiBon, or CRISPR/Cas9 inacBvaBon of the transcripBon factor coding genes Msx or Klf1/2/4/17 , median fin did not form. We postulated that this geneBc program should regulate effectors of tunic secreBon. We thus analyzed the expression and regulaBon in different ascidian species of two genes acquired by horizontal gene transfer (HGT) from bacteria, CesA coding for a cellulose synthase and Gh6 coding for a cellulase. Although we have uncovered an unexpected dynamic history of these genes in tunicates, and high levels of variability in gene expression and regulaBon among ascidians, we showed that Gh6 has a regionalized expression in the epidermis, and that it is a regulator of caudal fin formaBon. Our study consBtutes an important step in the study of the integraBon of HGT-acquired genes into developmental networks, and a cellulose-based morphogenesis of extracellular material in animals.