Ascidians possess relatively small and compact genomes. This feature enables us to easily isolate cis-regulatory DNAs of genes of interest. Particularly, cis-regulatory DNAs of genes showing tissue- or cell-type-specific expression are routinely used for the artificial induction of gene expression. This strategy helps us to label cells, tissues, and organs of interest, and to investigate gene functions through overexpression, ectopic expression, and the disruption of functions by dominant-negative forms. Thus, cis-regulatory DNAs provide a powerful tool for tissue-specific genetic manipulation in studies of ascidian development and physiology. This chapter summarizes the types of cis-regulatory DNAs as a genetic manipulation tool, describes the methods used for isolating cis-regulatory DNAs, and provide reported examples of the use of cis-regulatory DNAs as molecular tools for investigating gene functions.