Biological and ecological research is seriously handicapped because of difficulties experienced in the reliable detection and quantification of bivalve larvae. This is a critical issue in the case of the Manila clam Ruditapes philippinarum (Adams & Reeve, 1850), a largely invasive and commercially relevant species, with important wild, cultured, and naturalized populations throughout the world. A SYBR Green real-time PCR assay, containing TPHI16S1F and TPHI16S2R primers (specific to R. philippinarum female mtDNA), was designed and tested to provide a rapid and high-throughput PCR-based method for larval quantification. Accurate estimations of larval numbers in spiked plankton samples point to the usefulness of this system. It can be used through a wide range of evaluated variable experimental conditions, such as the presence of closely related bivalve species, stationary-dependent plankton abundance, sampling volumes, and larval size.