Arbuscular mycorrhizal (AM) symbiosis is a key plant-microbe interaction in sustainable ecosystems. Increasing land use intensity poses a threat to AM fungal communities, yet little is known of the impact of agricultural land use on AM fungal communities in many regions and cultivation types. The last few decades have witnessed increased cultivation of soybean worldwide with Argentina becoming one of the major producers. We compared the diversity and taxon composition of AM fungal communities in soybean fields in central Argentina with that in a natural Espinal forest under similar environmental conditions. We sequenced AM fungal DNA from root and soil samples collected from pairs of soybean fields and pristine forest ecosystems. We found that although AM fungal diversity tended to be lower in samples collected from the soybean field, the total number of AM fungal taxa was similar in both agricultural and forest ecosystems. Roots of soybean plants were colonized by diverse communities of AM fungi. AM fungal community composition in roots was primarily driven by host plant identity, but land use type (soybean field versus Espinal forest) was also an important determinant of community composition. The intensity of anthropogenic land use correlated with the proportion of easily-cultured AM fungal taxa, probably due to their efficient colonization strategies and better ability to recover from disturbance. Thus, soybean cultivation has affected AM fungal communities in terms of both diversity and functional attributes, although the diverse AM fungal communities are still present, probably due to the relatively low level of fertilizer application.