We analyzed arbuscular mycorrhizal fungal (AMF) communities in plant root samples from a natural forest ecosystem — a primeval forest in Järvselja, Estonia. AMF small-subunit (SSU) ribosomal RNA genes were subjected to 454-pyrosequencing and BLAST-based taxonomic identification. Seventy-six AMF sequence groups (virtual taxa, VT) were identified from plant roots. Taken together with seven additional VT recorded in an earlier investigation of soil AMF communities at the site, this represents the highest number of AMF reported from a single ecosystem to date. The six study plant species hosted similar AMF communities. However, AMF community composition in plant roots was significantly different from that in soil and considerably more VT were retrieved from roots than from soil. AMF VT identified from plant roots as a whole and from individual plant species were frequently phylogenetically clustered compared with local and global taxon pools, suggesting that nonrandom assembly processes, notably habitat filtering, may have shaped fungal assemblages. In contrast, the phylogenetic dispersion of AMF communities in soil did not differ from random subsets of the local or global taxon pools.