While the effect of disturbance on overall abundance and community composition of arbuscular mycorrhizal (AM) fungi has been researched in agricultural fields, less is known about the impact in semi-natural grasslands. We sampled two AM plant species, Festuca brevipila and Plantago lanceolata, from an ongoing grassland restoration experiment that contained replicated plowed and control plots. The AM fungal community in roots was determined using nested PCR and LSU rDNA primers. We identified 38 phylotypes within the Glomeromycota, of which 29 belonged to Glomus A, six to Glomus B, and three to Diversisporaceae. Only three phylotypes were closely related to known morphospecies. Soil disturbance significantly reduced phylotype richness and changed the AM fungal community composition. Most phylotypes, even closely related ones, showed little or no overlap in their distribution and occurred in either the control or disturbed plots. We found no evidence of host preference in this system, except for one phylotype that preferentially seemed to colonize Festuca. Our results show that disturbance imposed a stronger structuring force for AM fungal communities than did host plants in this semi-natural grassland.