Molecular Data generation of marine biodiversity data plays a central role in monitoring and better understanding of North Sea marine ecosystems. By applying DNA-based techniques, this study specifically aims to present a metabarcoding pipeline for Nanopore sequencing and compare a newly designed 2kb primer with commonly used MiFish pimer. eDNA samples were taken in The ray reef aquarium in Dolfinarium , The brokum reef ground in the North sea, at sany bottom, Gmini windpark and around 3 shipwrecks in the North Sea and analysed through metabarcoding with nanopore sequencing and results were compared with morphology and commonly used MiFish primer in order to demonstrate the value of applying this technique.