This is a technical guide for monitoring the taxonomic diversity of phytoplankton using environmental DNA metabarcoding, together with conventional phytoplankton monitoring techniques in marine and brackish waters. The guidelines focus on the detection of eukaryotic and prokaryotic phytoplankton with 185 and 165 rRNA primers, using high-throughput sequencing. Information and recommendations on sampling, sample processing, molecular biological work, quality control, bioinformatics, data storage and management and cost estimates are included so that the method eon be used to complement standardized light microscopy. Furthermore, the guidelines contain information from scientific literature and a discussion on future perspectives, including reference databases and standardization. The guidelines were developed within the project, lmplementing DNA-based methods in Northem European marine phytoplankton monitoring (/O­NEP), supported by the Nordic Council of Ministers in 2022. These guidelines serve as a status quo to accommodate future advances in molecular methods, international guidelines and standards. Using eDNA metabarcoding to complement standardized light microscopy advances conventional monitoring and research on phytoplankton communities to assess biodiversity and the state of the marine environment.