Global changes are initiating a cascade of complex processes, which result, among other things, in global climate warming. Effects of global climate change are most pronounced in the Arctic, where the associate processes are progressing at a more rapid pace than in the rest of the world. Intensified transport of warmer water masses into the Arctic is causing shifts in species distributions and efforts to understand and track these change are currently intensified. However, Arctic marine fauna is the result of different recurring colonization events by Atlantic and Pacific Ocean populations, producing a very confounding evolutionary signal and making species identification by traditional morphological taxonomic analysis extremely challenging. In addition, many marine species are too small or too similar to identify reliably, even with profound taxonomic expertise. Nevertheless, the majority of current research focusing on artic marine communities still relies on the analysis of samples with traditional taxonomic methods, which tends to lack the necessary taxonomic, spatial and temporal resolution needed to understand the drastic ecosystem shifts underway. However, molecular methods are providing new opportunities to the field and their continuous development can accelerate and facilitate ecological research in the Arctic. Here, we discuss molecular methods currently available to study marine Arctic biodiversity, encouraging the DNA barcoding for improved descriptions, inventory and providing examples of DNA barcoding utilization in Arctic diversity research and investigations into ecosystem drivers.