To explore if there are species-preferential characteristics of arbuscular mycorrhizal (AM) and host plants in karst regions, 13 shrub plants (including leguminosae and non-leguminosae) were selected to study the AM community structure of root samples. The soil nutrients in rhizosphere soils significantly differ among shrubs; they are higher in leguminosae than in non-leguminosae. Cluster analysis shows that all 13 shrubs can be infected by AM. Significant differences of the AM community structure were observed among root samples from different shrubs, especially leguminosae and non-leguminosae. Redundancy analysis shows that soil Olsen-P, pH, and total nitrogen significantly influence the AM community structure of plant roots, although the factors affecting this fungus in leguminosae and non-leguminosae differ. These results indicate species-preferential characteristics of AM and host plants in karst regions, especially of the plant function group compared with plant species, suggesting that these characteristics should be taken into account when AM fungi are used for vegetation restoration in karst regions.