Using a polymerase chain reaction (PCR)-generated gene fragment as a probe, we isolated and sequenced a gene encoding an actin-related protein belonging to the Arp3 family from the pufferfish, Fugu rubripes. The Fugu Arp3 gene spans 3.7kb from the transcription start site to the polyadenylation signal. This is the first report of the genomic sequence of a vertebrate Arp3 gene. The Fugu Arp3 gene consists of 12 exons and 11 introns compared to Drosophila homologue, which has six exons and five introns. The protein sequence encoded by the Fugu gene is 97% and 80% identical to bovine and Drosophila homologues, respectively. The Fugu Arp3 gene is expressed in a wide range of tissues, with higher levels detected in the gills, kidney, ovary, skin and testis. Three different size transcripts of the Arp3 gene (1.4kb, 1.8kb and 2.2kb) were identified in various tissues.