The study describes the primary assembly of arbuscular mycorrhizal communities on a newly constructed island Peberholm between Denmark and Sweden. The AM fungal community on Peberholm was compared with the neighboring natural island Saltholm. The structure of arbuscular mycorrhizal communities was assessed through 454 pyrosequencing. Internal community structure was investigated through fitting the rank-abundance of Operational Taxonomic Units to different models. Heterogeneity of communities within islands was assessed by analysis of group dispersion. The mean OTU richness per sample was significantly lower on the artificial island than on the neighboring natural island, indicating that richness of the colonizing AM fungal community is restricted by limited dispersal. The AM fungal communities colonizing the new island appeared to be a non-random subset of communities on the natural and much older neighboring island, which points to high colonization potential of certain – probably early successional – mycorrhizal fungi, likely assisted by migratory birds.