Urochordates or tunicates possess a notochord, dorsal neural tube, and gill slits, features characteristic of all chordates, and thus they are a sister group of vertebrates, including humans. Urochordates consist of larvaceans, ascidians, and thaliaceans. The draft genome has been decoded in ascidians, Ciona intestinalis and C. savignyi. The C. intestinalis genome is composed of approximately 160 Mbp, similar to other invertebrate genomes, and contains approximately 16,000 protein-coding genes that represent the basic set of chordate genes without the extensive gene duplications seen in vertebrates. The C. intestinalis gene models are intensively annotated and supported by corresponding cDNAs. With the aid of two-color fluorescent in situ hybridization of BAC clones, approximately 65% of the assembled genome information has been mapped onto the 14 pairs of C. intestinalis chromosomes. In addition, a genome project is ongoing in a larvacean, Oikopleura dioica, and its genome is estimated to be 60 Mbp, with a very compacted arrangement of genes. Although the urochordate genomes have lineage-specific innovations such as horizontal acquisition of the cellulose synthase gene from bacteria and spliced-leader trans-splicing of mRNAs, applicable modern techniques have made urochordates serious contenders in the illumination of the basic principles underlying genome dynamics of vertebrates.