Managing natural resources in a sustainable manner requires understanding the complexity of ecosystems and the species that are associated with the different parts of the ecosystem. Much of this knowledge is derived from traditional sampling methods (e.g., different types of trawls). The analysis of environmental DNA (eDNA) can provide increased knowledge, complementary to the traditional methods. In the present pilot study, we sampled eDNA from two geographical areas, north and west of Svalbard (NWS) and in the southwestern Barents Sea (SWBS). The combination of trawling, visual identification of mammals and eDNA collection facilitated a robust analysis of fish and marine mammal diversity and species composition. Through 12S MiFish metabarcoding of the eDNA samples, we found that incorporating eDNA data provided an additional level of information on both the diversity of fish and marine mammals in the study areas. By adding eDNA data to the trawl data, we found that richness increased from 32 to 49 fish taxa. Significant differences in diversity and composition of the fish communities were detected by eDNA between the two study areas. Considering degradation and dilution factors it is postulated that the results represent resident species to the Barents Sea and that long -transported DNA from other areas are less likely.