The Arctic is changing rapidly, exemplified by elevating temperatures and a reduction in sea ice extent and thickness. These climate-induced changes put an increasing pressure on the Arctic ecosystem and its populations, including the most abundant circumpolar marine fish polar cod (Boreogadus saida). As a keystone species, changes in its abundance and distribution will impact the entire Arctic food web. Despite of significance, its population structure is largely undescribed. Therefore, the genetic diversity and population connectivity of polar cod living in fjords of West-Spitsbergen and the Eurasian Basin were investigated using eight microsatellite loci. On a local scale, polar cod from Arctic (Billefjorden) and Atlantic (Kongsfjorden) influenced fjords were compared, and on a larger scale also specimens from the Amundsen and Nansen Basin were included. Juvenile polar cod track sea ice drift and consequently, the under-ice distribution depends on coastal populations where sea ice originates. Results revealed significant population structuring between Billefjorden and Kongsfjorden (FST=0.052). On a larger scale, polar cod from Kongsfjorden and Amundsen (FST=0.017) and Billefjorden and Nansen Basin (FST=0.059) were genetically differentiated, suggesting reduced gene flow between these areas. Hypothetically, polar cod hatched in the Kara and Laptev Sea drift into the Nansen and Amundsen Basin, respectively, and settle west of Spitsbergen by following the Transpolar Drift System. Polar cod hatched in the Laptev Sea may prefer less saline, Arctic fjords. Full knowledge of population connectivity is necessary for management and conservation purposes in a quickly changing environment.