Jellyfish have been hypothesized to thrive as winners of climate change. Abundances of several jellyfish species are expected to grow, and this could be particularly the case in areas of rapid change, such as the warming Arctic waters. Despite the increased number of reported jellyfish blooms and their negative effects on fisheries worldwide, jellyfish remain an understudied part of zooplankton due to their fragility and their reputation as "trophic dead end". This study aims to investigate the two scyphozoan jellyfish species Periphylla periphylla and Cyanea capillata, both of which hypothesized to expand their distribution ranges poleward. The analysis consists of three parts: first, the intraspecific diversity of the two species was investigated using DNA barcoding of samples from Svalbard, Greenland, and Norway. Second, to characterize the status quo of high-Arctic jellyfish species diversity, we applied eDNA metabarcoding of sediment samples around Svalbard. Moreover, the efficiency of this method to reveal pelagic communities was compared with net catches in the same stations. Lastly, species-specific primers were developed and tested, with the future aim to optimize quantitative real-time PCR as a cost-effective and accurate tool for detecting the target species from environmental samples. The study revealed a high intraspecific genetic diversity and a lack of geographic structure in both species. C. capillata was shown to consist of three species-level lineages with overlapping distributions, and the cluster identified as C. capillata showed a higher genetic diversity than P. periphylla. We discussed these patterns of genetic diversity in the light of the life cycles of both species. The metazoan species diversity revealed with the metabarcoding analyses of the Svalbard sediment samples did not represent the pelagic community well, compared to net and trawl catches from the same stations. Many of the zooplankton and especially jellyfish species caught with nets were not represented in the eDNA. Overall, differences in species diversity between the West Svalbard and North Svalbard fjords could be observed, for different metazoan groups, including Cnidaria. In the northern fjords, consistently more cnidarian species were found, indicating the important role jellyfish have in Arctic communities. We discussed our results with other studies of zooplankton diversity in Atlantic and Arctic waters. The design of a species-specific primer was successful for C. capillata on all levels of testing, from tissue DNA extract to environmental samples. Overall, this study shows the importance of investigating jellyfish with modern molecular tools, which may help to inform us on their potential range expansions or population increases in the future. Additionally, we provide guidelines for future research on the topic, based on our study design.