Invasive marine species (IMS) are a major anthropogenic threat to global marine environments. To mitigate the threat, Australian federal and state governments have developed detailed quarantine programs to minimise IMS introductions, supported by monitoring programs to detect any IMS that penetrated the quarantine barriers. Considerable shipping movements occur between the Pilbara region of northwestern Australia and southeast Asia where a number of potential IMS oysters occur. eDNA techniques are being developed to rapidly scan biofouling and other samples for potential IMS, but there is limited information on oysters present in the Pilbara. We collected intertidal oysters in and near Pilbara ports and identified them using DNA sequences to determine if any IMS are present and to provide a baseline to prevent false positive results for IMS by native species. Only three species were detected: native Saccostrea lineage A and S. scyphophilla, both widespread in the Pilbara, and Talonostrea sp. nov. which had not previously been reported from the Pilbara. No IMS oysters were found. The study provides a solid basis for monitoring for any future occurrences of IMS oyster species in the Pilbara, an area with a very high known shallow water marine biodiversity, but where only a single IMS is known to occur.