Echinococcus multilocularis is an endemic parasite of red foxes in several European countries. This parasite has been present for decades in central Europe i.e. Switzerland, Eastern France, Southern Germany and Austria, which constitute the core endemic area of Europe. In the Scandinavian countries Sweden and Denmark, several recent findings were made in foxes. To better understand the dynamics and geographic spread of E. multilocularis in Europe, genetic studies have been undertaken using the DNA microsatellite marker EmsB. In Europe, the parasite spread in hitherto non-endemic areas was suspected to take place after founder events, in which the core endemic area presents a wider genetic diversity in comparison to newly endemic areas. However, identical parasite profiles can be shared between them, highlighting the parasite spreading in a mainland-island system. In this study, Swedish (27 adult worms from seven red foxes) and Danish (38 adult worms from nine red foxes) isolates were examined using fragment size analyses of the tandemly repeated microsatellite EmsB in order to compare the genetic profiles of the Scandinavian worms with a reference collection of European worm isolates from seven countries. Six EmsB profiles were detected in the Scandinavian panel. Three profiles were described in Denmark and four in Sweden. Only one of these profiles was detected in both countries. All profiles identified in the present study have previously been found in other European countries, suggesting an epidemiological link. Due to the relatively low number of Scandinavian E. multilocularis isolates analysed so far, firm conclusions cannot be made regarding the true genetic diversity. Nevertheless, the low genetic variation detected in Sweden and Denmark in this study is similar to the values obtained from peripheral areas of the main European endemic focus, which were more recently colonized by E. multilocularis; and continuous surveillance of this parasite is warranted to provide further insight into its epidemiology in Scandinavia.