Echinococcus multilocularis is a threatening cestode involved in the human alveolar echinococcosis. The parasite, mainly described in temperate regions of the Northern hemisphere was described for the first time in 1999 in the High Arctic Svalbard archipelago, Norway. The origin of this contamination could be due to an anthropogenic introduction from mainland Europe by domestic dogs or with the introduction of the sibling vole, perhaps from mainland Russia (St. Petersburg area), or with roaming Arctic foxes, known as the main definitive host of the parasite in Arctic regions. The genetic diversity of E. multilocularis in Svalbard was investigated here for the first time by genotyping using EmsB microsatellite and compared to other genotyped populations in the main worldwide endemic areas. We found low polymorphism amongst the 27 metacestode isolates from sibling voles trapped in the core of the distribution area of the vole on Svalbard. E. mutilocularis Arctic populations, using the Arctic fox as the definitive host, were genetically separated from European temperate populations that use the red fox, but closely related to St. Lawrence Island samples from Alaska. The result is inconsistent with the hypothesis of an anthropogenic introduction from mainland Europe, but can be seen as consistent with the hypothesis that Arctic foxes introduced E. multilocularis to Svalbard.