The Water Framework Directive 2000/60/EC regulates the environmental diagnosis of the marine ecosystem, including the evaluation of species of bioindicator macroinvertebrates present in the environment. To date, these types of determinations are carried out through the morphotaxonomic identification of the benthic macrofauna present in the samples and the calculation of associated biotic indexes, a process that is time-consuming and resource-intensive, being in some cases inaccurate due to the requirement of highly specialized human resources and the difficulty of correctly identifying certain species. In this respect, DNA barcoding techniques allow the reliable identification of organisms using DNA sequencing techniques and avoiding the disadvantages of morphotaxonomic identification. On the other hand, the recent development of New Generation DNA Sequencing techniques (NGS) has allowed the development of DNA metabarcoding, i.e. the characterization of populations of organisms present in a sample using genomic data. This paper shows the fundamental challenges to be overcome in order to establish a NGS sequencing-based assessment of the marine environmental quality.