The detection of invasive species soon after an incursion, when the population is confined to a small area and at a low density, maximizes the probability of successful eradication. In response a number of sensitive molecular methods have been developed for identifying the larvae of marine invertebrate pests at extremely low concentrations. In this study we developed a highly sensitive real-time PCR assay targeting the 18S ribosomal DNA for the rapid and accurate identification of the Asian clam Corbula amurensis in environmental samples. Larvae of C. amurensis were spiked into commonly encountered sampling matrices including benthic assemblages, biofilms, sediment grabs and plankton net hauls, and the sensitivity of the assay was assessed. In this study the assay reliably detected one larva in up to 10 g of sediment, and five larvae in 10 g of benthic invertebrate and macro-algal assemblages. Seawater and benthic assemblage samples were collected from four major ports around New Zealand and all were negative for C. amurensis using the real-time PCR assay. This assay has the potential to enhance current surveillance methods, especially regarding morphologically difficult to identify early life-stages. Real-time PCR can be used with high through-put platforms and is extremely sensitive, increasing detection potential during initial stages of incursions.