As the genomes of increasing numbers of organisms are sequenced, the value of new sequence data is enhanced when the process that is used to assign names to the sequenced genes is clear and consensual. The optimum time to erect a naming system for any taxonomic group is early in the expansion of the genome databases. In spite of being one of the major metazoan phyla, the Mollusca (~93,000 living species) are latecomers to the field of genomics. As molluscs include species that are used as food, others that transmit human diseases, or serve as biomedical models, or play important roles in both terrestrial and aquatic ecosystems, or are admired for their esthetic qualities, a marked increase in genomic data is anticipated. As the first sequenced molluscan genomes (a snail Biomphalaria glabrata, and a bivalve Crassostrea gigas) will have been released in 2012, a convention is proposed to establish a clear process and a rational naming system. The molluscs comprise one major grouping within the metazoan Lophotrochozoa, so the convention may prove to be of value for a wider array of related taxa.