DNA metabarcoding methods have been implemented in studies aimed at assessing and quantifying marine benthic biodiversity. In such studies, first DNA is extracted from environmental samples, then target barcodes are amplified and subsequently sequenced. In order to use such methods in a quantitative manner, a relation between the biomass and/or the abundance of a species and the number of its DNA sequences is assumed. However, studies validating this relationship are rare. In this study, we validate measurements of biomass and abundance between traditional morphological and molecular approaches. A total of 126 samples from a benthic intertidal system were analysed and quantified using abundancy and biomass estimates from the morphological approach and frequency of occurrence and relative read abundance estimates from the molecular approach. A relationship between biomass and relative read abundance was only found for one taxon (Pygospio) but all other taxons failed to show such a relationship. We discuss how quantitative measurements by the molecular approach are hampered by the ecology of DNA, i.e., all the processes which determine the amount of DNA in the environment including the ecology of the benthic species.