Jellyfish abundances have been reported to increase significantly in different aquatic ecosystems. Particularly in areas of rapid change such as the warming Arctic waters, jellyfish blooms might occur more frequently and cause problems for local fisheries. However, until today jellyfish remain an understudied part of zooplankton due to their fragility and historically proposed irrelevance in marine food webs. This study aims to investigate the genetic diversity of the two species Periphylla periphylla and Cyanea capillata using a set of molecular methods. To monitor future range expansions, we aim to validate eDNA as a viable detection method for jellyfish. The analysis consists of three parts: first, the intraspecific genetic diversity of the two species is investigated using DNA barcoding. Second, to characterize the status quo of high-Arctic jellyfish species diversity, we apply eDNA metabarcoding of sediment samples around Svalbard. Lastly, species-specific primers are developed and tested, with the aim to optimize quantitative real-time PCR as a cost-effective, accurate monitoring. A high intraspecific genetic diversity has been shown in the studied area for both species. For C. capillata three divergent species-level lineages were uncovered. Genetic structure according to geographic region was lacking for both species. The metabarcoding analyses of the Svalbard sediment samples did not represent the pelagic community well, compared to net catches from the same stations. Many of the zooplankton and especially jellyfish species caught with nets were not represented in the eDNA. However, differences in pelagic species composition could be observed between North and West Svalbard fjords. In the Arctic-influenced fjords, consistently more jellyfish species were found. The design of a species-specific primer was successful for C. capillata. This study shows how important it is to investigate jellyfish with modern molecular tools, which may help to inform us on their potential range expansions or populations increases in the future.