Microinjection is a common technique used to deliver nucleic acids into eggs and embryos in Ciona species. There are three Ciona species that are commonly used for research-Ciona intestinalis type A (C. robusta), C. intestinalis type B (C. intestinalis), and C. savignyi. Here, we present the microinjection methods using eggs and embryos of C. intestinalis type A and C. savignyi; however, our methods would also be applicable to eggs and embryos of C. intestinalis type B. Microinjection is a classical and widely used delivery method, which involves the use of a glass micropipette, a hollow glass needle with a microscopic tip, to inject nucleic acids into eggs and embryos under a stereo microscope. The required amount of nucleic acids is much smaller for microinjection than for electroporation, another delivery method. Proteins, and other chemicals, such as fluorescent dye, can be introduced with nucleic acids using a microinjection.