The range of ecological roles exhibited by arbuscular mycorrhizal (AM) fungi depends on functional differences among naturally occurring local assemblages of AM species. While functional differences have been demonstrated among AM fungal species and among geographic isolates of the same species, almost nothing is known about functional differences among whole communities of naturally occurring AM fungi. In the greenhouse, we reciprocally transplanted whole AM fungal communities between plant–soil systems representing a serpentine grassland and a tallgrass prairie, using as hosts two grasses common to both systems. For Sorghastrum nutans, native fungi consistently enhanced plant growth more than fungi switched from the alternate system. For Schizachyrium scoparium, foreign and native fungi promoted plant growth similarly in both the serpentine and prairie systems. Thus, the use of foreign inoculum in restoration could change the relative performance, and potentially the competitive abilities, of co-occurring plant species. Moving AM fungal inocula into foreign environments also caused changes in the taxonomic composition of the resultant spore communities, demonstrating their response to environmental influences. These results provide strong evidence for functional differences among naturally occurring AM communities and suggest that a particular AM fungal community may be better matched ecologically to its local habitat than communities taken from other locations.