The ascidians occupy a crucial phylogenetic position between invertebrates and vertebrates. Advances in molecular biological techniques and molecular cloning have enabled studies of molecular mechanisms to be more and more accessible in ascidians. Recently, an increasing number of ascidian genes have been cloned. In this review, we summarize the molecular features and expression profiles of all ascidian genes published to date and describe how and why they were cloned. Such information not only is valuable for understanding the recent advancements in ascidian molecular biology but also to bring out the importance of ascidians as an experimental system for a variety of fields in biology.