The Rel/NF-κB transcription factors can function as key regulators to modulate the expression of immune-related genes in response to immune challenge or environmental stress. In the present study, a gene coding Rel/NF-κB homologue was identified from scallop Chlamys farreri (designated CfRel). Its deduced protein comprised 359 amino acids, and contained a conserved N-terminal Rel homology domain (RHD) and an IPT domain. There was an NF-κB/Rel/dorsal domain signature sequence in the RHD domain. The mRNA transcripts of CfRel could be detected in all the tested tissues including adductor muscle, mantle, gill, gonad, haemocytes, kidney and hepatopancreas, with the highest expression level in hepatopancreas. After LPS stimulation, there were two peaks of CfRel mRNA expression level in haemocytes at 6 h (25.25-fold, P < 0.05) and 24 h (59.66-fold, P < 0.05) respectively, while the mRNA expression of CfRel was only up-regulated at 3 h after PGN stimulation (2.35-fold, P < 0.05). By Western blotting technique, CfRel protein was observed in the cytoplasm and nucleus of scallop haemocytes, and its concentration in the haemocyte nucleus increased significantly at 3 h and 12 h after LPS stimulation. The noticeable NF-κB transcription activity of CfRel protein was determined by NF-κB luciferase reporter assays (122.43%, P < 0.05), and it decreased significantly (17.61%, P < 0.05) after the coexpression of scallop IκB protein. These results collectively suggested that CfRel mRNA transcripts and protein were induced by immune stimulation, and CfRel protein could extricate itself from IκB protein and transfer into the haemocyte nucleus to modulate the immune response in scallop.