Tunicates are invertebrate members of the chordate phylum, and are considered to be the sister group of vertebrates. Tunicates are composed of ascidians, thaliaceans and appendicularians. With the advent of inexpensive high throughput sequencing, the number of sequenced tunicate genomes is expected to rise sharply within the coming years. To facilitate comparative genomics within the tunicates, and between tunicates and vertebrates, standardized rules for the nomenclature of tunicate genetic elements need to be established. Here we propose a set of nomenclature rules, consensual within the community, for predicted genes, pseudogenes, transcripts, operons, transcriptional cis-regulatory regions, transposable elements, and transgenic constructs. In addition, the document proposes guidelines for naming transgenic and mutant lines. The latest version of these guidelines can be downloaded from the Tunicate Portal (http://www.tunicate-portal.org/). To better identify the latest version, the file name for the guidelines should follow the following syntax: Genetic_Guidelines_Tunicate_[year]_[month]_[day] (example, Genetic_Guidelines_Tunicate_2014_05_01). © 2014 Wiley Periodicals, Inc.