Synaptonemal complex protein 3 (SCP3) is a meiosis-specific component of the synaptonemal complex essential for gametogenesis. In vertebrates, SCP3 protein is specifically localized in primary spermatocytes and many researchers have used it as a molecular marker to identify and separate primary spermatocytes from all types of germ cells. To measure whether SCP3 can mark any specific germ cells in invertebrates, we cloned a 1 033 bp full-length cDNA of Chlamys farreri SCP3 (Cf-SCP3) that contains a 726 bp open reading frame encoding 241 amino acids with one conserved Cor1 domain and two coiled-coil domains. Then we synthesized the DIG-labeled RNA probe, expressed the Cf-SCP3 recombinant protein and generated the anti-Cf-SCP3 polyclonal antibody. In situ hybridization and immunohistochemistry observations showed that Cf-SCP3 transcripts and Cf-SCP3 protein were specifically expressed in primary spermatocytes and unfertilized eggs, while no expression was detected in any other spermatogenic cells or ovarian cells of C. farreri. Thus, it suggested that the Cf-SCP3 protein might participate in meiosis of gametogenesis as a component of the synaptonemal complex like that in vertebrates and could be used as a candidate molecular marker for identifying the primary spermatocytes in germ cells differentiation study of C. farreri.