Monitoring species distributions and biodiversity is the fundamental basis for ecological studies and biodiversity management. Obtaining such detailed information is often difficult due to the limitations of current monitoring tools that are often time-consuming and expensive. Also, monitoring can be especially problematic from a management perspective since most environmental agencies focus their efforts on species present at low densities, such as recently introduced or spreading Invasive Alien Species (IAS) and rare or threatened native species. Recent advances in extracting environmental DNA (eDNA), DNA barcoding and sequencing technologies now make it possible to analyse whole species communities by extracting and analysing eDNA fragments (eDNA metabarcoding). Here we propose an eDNA-based methodology that can potentially be used for the monitoring of entire fish communities. By carefully selecting the target fragments, PCR primers and PCR blocking primers we expect to be able to develop a highly sensitive, accurate and reliable eDNA metabarcoding tool. The developed methodology is expected to significantly improve monitoring surveys and will be tested in the field to evaluate the effects of a spreading population of invasive fish on the native fish community. The ultimate goal of this research would be to deliver an eDNA metabarcoding tool that can be used to improve the monitoring and management of invasive and rare or threatened native species.