The European Marine Omics Biodiversity Observation Network (EMO BON) is an initiative of the European Marine Biological Resource Centre (EMBRC) to establish a persistent genomic observatory among designated European coastal marine sites, sharing the same protocols for sampling and data curation. Environmental samples are collected from the water column, and at some sites, soft sediments and hard substrates (Autonomous Reef Monitoring Structures - ARMS), together with a set of mandatory and discretionary metadata (including Essential Ocean Variables - EOVs). Samples are collected following standardized protocols at regular and specified intervals, and sequenced in large six-monthly batches at a centralized sequencing facility. The use of standard operating procedures (SOPs) during data collection, library preparation and sequencing aims to provide uniformity among the data collected from the sites, coupled with strict adherence to open and FAIR (Findable, Accessible, Interoperable, Reusable) data principles, ensures maximum comparability among samples and enhance reusability and interoperability of the data with other data sources. The observatory network was launced in June 2021, when the first sampling campaign took place.