Natural England (NE) and the Joint Nature Conservation Committee (JNCC) jointly commissioned these reports to provide a review and protocol for benthic sampling in the context of eDNA metabarcoding and long-term monitoring in UK Marine Protected Areas. This was with a particular focus on statutory monitoring of benthic species and habitats of conservation importance. DNA-based methods for species detection and identification have transformed our ability to monitor biodiversity in both aquatic and terrestrial systems. Traditional morphological identification is currently the primary tool for biodiversity assessment for benthic sampling. Introducing standardised marine benthic DNA sample collection and processing across SNCBs’ marine surveys (with different spatial and temporal scales) could provide considerable benefits in terms of cost savings, sample turnaround times, and a massive increase in the amount of biodiversity data collected per sample. The scope of this review was limited to the collection and preservation of benthic sediment samples, including macrofauna separated from sediment, in the context of eDNA metabarcoding. The protocol is not intended to replace existing field subtidal sediment sampling methodologies for macrofaunal invertebrates but to identify the most suitable operational eDNA sampling protocols that can be applied alongside existing sediment sampling approaches conducted by JNCC and NE. This review outlines the current state of the field in DNA-based marine benthic biomonitoring to enable scientists and managers to make informed decisions and to maximise the benefits of this new technology.