Host specificity among ectomycorrhizal (ECM) fungi seems to vary among different habitats, and it is difficult to draw general conclusions across environments. Little is known about the host specificity among arctic ECM fungi. In this study, we investigated the host specificity of root associated fungal communities in three different EMC forming host plants using 454-sequencing of tag encoded ITS1 amplicons. We sampled the entire root systems of 20 plants each of the three ECM species Bistorta vivipara, Dryas octopetala and Salix polaris in two plots in the arctic archipelago Svalbard. The root systems were dominated by the Basidomycota both concerning number of OTUs (74%) and especially number of reads (95.7%). No host specificity was found among the root associated fungal communities, nor among fungi with taxonomic affiliation to known ECM fungi. Moreover, the fungal richness did not vary significantly among the three plant host species despite extensive variation in root size. No spatial autocorrelation was observed, which may indicate a lack of extensive common mycelial networks in the arctic.