New strategies for embryonic manipulation have been developed in recent years through plant and animal research. However, research on marine invertebrate embryos has suffered from a lack of basic tools, such as microinjection. Here we present a technique developed for microinjecting eggs and embryos of the oyster Crassostrea gigas and the mussel Mytilus edulis. In experimental trials, approximately 40% of microinjected embryos survived. This technique was used to microinject β-galactosidase, for which specific detection techniques were developed. A reporter construct (CMV-β) based on a promoter of cytomegalovirus linked to the β-galactosidase-encoding gene was then microinjected, and the expression level of this construct was monitored. The suitability of this technique is discussed in terms of its application to the manipulation of bivalve mollusks in pathology and genetics.