The rapid rate of warming affecting the Arctic is causing unprecedented changes to the marine communities inhabiting this region. Gelatinous zooplankton or jellies span several distantly related groups (ctenophores, cnidarians and tunicates) and have previously been overlooked as potential key components of this polar ecosystem. In warmer waters jellies have been known to rapidly increase in biomass forming jelly blooms with potentially harmful consequences. Therefore, understanding the role of jellies in Arctic ecosystems is key to predict the consequences of warming temperatures not only for jellies but other species in the Arctic food web. The ctenophore family Beroidae is of particular importance due to their role as a predator of other gelatinous zooplankton, thereby helping control their abundances, as seen with Beroe ovata for Mnemiopsis leidyi in the Black Sea. Understanding the distribution of this predator will help predict its future role and significance in Arctic food webs. To assess potential factors influencing the distribution patterns of Beroe species in the Arctic, this study focusses on the widely distributed Beroe cucumis and the deeper dwelling Beroe abyssicola. Recent papers have attempted to uncover the phylogeny and genetic connectivity of ctenophore species, including Beroe. However, due to standard cytochrome-c-oxidase subunit 1 (COI) primers not working for ctenophores and other markers such as 18s not yielding the resolution necessary, the phylogeny of Beroidae remains unclear. Applying newly published primers for COI, in addition to ITS1, this study compares the genetic structure and connectivity revealed by one nucleic and one mitochondrial marker. Genetic diversity indices, hierarchical population structure and demographic history were determined for samples from Greenland, Svalbard and mainland Norway. Evaluating the congruence between the different markers will help understand not only the population structure of the two species, but also the potential for these markers in future genetic studies of Beroe.