Long-chain polyunsaturated fatty acids (LC-PUFAs) are essential in lots of important physiological processes, while, many marine species have no or limited ability of endogenous PUFA biosynthesis, normally due to the lack of key enzymes such as fatty acid desaturase (FAD). In this study, we isolated a scallop Chlamys nobilis cDNA with high homology to vertebrate FADs. Functional characterization in recombinant yeast Saccharomyces cerevisiae showed that scallop FAD exhibited Δ5-desaturation activity towards both saturated and PUFA substrates. Thus, it efficiently desaturated exogenously added PUFA C20:4(n - 3) and C20:3(n - 6) to C20:5(n - 3) (EPA) and C20:4(n - 6) (ARA) respectively. It also converted the yeast's endogenous C18:0 into C18:1(n - 13), and participated in the biosynthesis of non-methylene-interrupted FA by introducing a double bond to C20:3(n - 3) and C20:2(n - 6) in the Δ5 carbon. Temporal transcript profile of scallop FAD was studied during early embryonic development. High level of mRNA was found at the beginning of embryogenesis (egg) and noticeable decreases of were observed during larvae development, suggesting maternal FAD mRNA transfer to the embryo. Further, FAD transcripts were detected in all tissues analyzed, with the gonad and hepatopancreas showing the highest expression.