Apoptosis plays significant roles in maintenance of homeostasis, immune defense and development. The Bcl-2 family proteins are important regulators of the intrinsic apoptosis. In the study, we have characterized a Bcl-2-like gene (named CfBcl-2) and a Bax-like gene (named CfBax) from the Zhikong scallop Chlamys farreri. The full-length of the CfBcl-2 cDNA is 944 nucleotides (nt) encoding a putative protein of 225 amino acid residues (aa) that contains four Bcl-2 homology (BH) domains, and the CfBax cDNA is 505 nt encoding a putative protein of 115 aa that contains three Bcl-2 BH domains. Sequence and phylogenetic analysis demonstrate that CfBcl-2 and CfBax present typical domain organization of the corresponding Bcl-2 related proteins and are more similar and clustered with their homologues of other molluscs. The two genes are ubiquitously expressed in six tissues of C. farreri, with the highest expression level of CfBcl-2 in adductor muscle and highest expression level of CfBax in gill. The expressions of CfBcl-2 and CfBax in hemocytes were both significantly up-regulated after an in vivo exposure of scallops to air, injection with lipopolysaccharide and infection with acute viral necrobiotic disease virus, and the expression patterns of the two genes after the three treatments vary in different change magnitude and up-regulation timespan. Yeast two-hybrid assay reveals a direct interaction between the CfBcl-2 and CfBax proteins. These results indicate that the CfBcl-2 and CfBax may participate in the apoptosis-based stress and immune responses against noxious stimulation.