Transcription factor Rel/nuclear factor-kappa B (NF-kappaB) has been the focus of many studies since its discovery in 1986. Different homologs of Rel/NF-kappaB have been found in both vertebrate and invertebrate. A cDNA clone encoding a putative Rel/NF-kappaB homolog (designated Pf-Rel) was isolated from the pearl oyster, Pinctada fucata. The sequence of Pf-Rel consists of the Rel homology domain, IPT NF-kappaB domain and C-terminal transactivation domain. Sequence analysis of Pf-Rel shows that it shares high similarity with other Rel/NF-kappaB family proteins, especially within the conserved domains. Reverse transcription-polymerase chain reaction analysis revealed that Pf-Rel mRNA was expressed ubiquitously. Further in situ hybridization analysis showed that Pf-Rel mRNA was expressed mainly at the outer epithelial cells of the middle fold and the inner epithelial cells of the outer fold. The identification and characterization of pearl oyster Pf-Rel help to further investigate the involvement of Rel/NF-kappaB in oyster immunity and other biological processes.