The Arctic is experiencing increasing water temperatures, leading to a northward shift of Atlantic species into Arctic waters. Arctic marine ecosystems are therefore subject to sub- stantial changes in species distributions and occurrence due to anthropogenic climate change. Atlantic cod is one of the most important commercial fish species in the northern seas. The largest known stock is the migrating Northeast Arctic cod (NEAC) that is distributed along the Norwe- gian coast, the Barents Sea and off Svalbard. Atlantic cod in Svalbard waters are generally reported in the literature as belonging to the NEAC ecotype. The more stationary coastal cod (CC) spawn together with NEAC in the Lofoten region and several other areas along the Norwegian coast. The aim of this study was to investigate the population structure of Atlantic cod in Svalbard waters. We used single nucleotide polymorphic (SNP) markers, the pantophysin locus (Pan I) and otolith structure to categorize the 2 cod ecotypes collected in Svalbard fjords between 2017 and 2019. Our results show that both NEAC and CC appear in Svalbard fjords and revealed that 0- group and adult CC individuals caught in Svalbard fjords differ genetically from those along the Norwegian coast, indicating a separation into a local Svalbard CC population. The establishment of CC in Svalbard fjords may be another keystone of the ongoing borealization of the Arctic, with consequences for the local Arctic fjord ecosystem.