FOXL2 is a member of the forkhead box family, a transcription factor essential for the early regulation of ovarian development that is expressed in a sexually dimorphic manner in vertebrates. However, data on this gene in invertebrates are rare. In this study, we cloned a full-length cDNA sequence of foxl2 from the scallop Chlamys farreri, an important commercial mollusk in China. The cDNA sequence of Cf-foxl2 (C. farreri foxl2) has 1,824 bp with an open reading frame of 1,107 bp encoding 369 amino acid residues containing the conserved domain forkhead box. Semiquantitative RT-PCR showed that Cf-foxl2 was expressed mainly in the ovary. Using quantitative real-time PCR, we found that the highest expression was in the ovary of proliferative stage animals, about 62-fold higher than that in the testis and about twofold higher than that in the ovary of growing and mature stages. In situ hybridization revealed that Cf-foxl2 mRNA was located in the cytoplasm of follicle cells and germ cells in the ovary and testis except in the spermatozoa. Our data imply that Cf-foxl2 is expressed in a sexually dimorphic pattern at the RNA level, which is conserved with vertebrates.