This laboratory manual details protocols for detecting marine invasive species using eDNA sampling from the PacMAN project. These are the standard operating procedures shared with the stakeholder community. Field protocols describe the collection of environmental DNA samples (water, settlement plates, plankton) as well as specimens for subsequent analysis. Safety procedures and laboratory rules are extensively covered, emphasising safe handling of potentially hazardous materials and equipment. Laboratory procedures outline sample processing, DNA extraction, PCR amplification, and quality checks, culminating in next-generation sequencing library preparation. Finally, data management and bioinformatics aspects are addressed briefly.