Transgenesis is an indispensable method for elucidating the cellular and molecular mechanisms underlying biological phenomena. In Ciona, transgenic lines that have a transgene insertion in their genomes have been created. The transgenic lines are valuable because they express reporter genes in a nonmosaic manner. This nonmosaic manner allows us to accurately observe tissues and organs. The insertions of transgenes can destroy genes to create mutants. The insertional mutagenesis is a splendid method for investigating functions of genes. In Ciona intestinalis, expression of the gfp reporter gene is subjected to epigenetic silencing in the female germline. This epigenetic silencing has been used to establish a novel method for knocking down maternal expression of genes. The genetic procedures based on germline transgenesis facilitate studies for addressing gene functions in Ciona.