Arbuscular mycorrhizal (AM) fungi have important functions, and these functions are different among AM fungal species; therefore, study of AM fungal diversity and their impact on their host plants are important. Complementary/redundant functions in nutrient acquisition among AM fungal hyphae and plant roots were proposed by Koide (2000), but this concept has not been well tested. In this research, interactions among AM fungi and their impact on plant growth were examined using the conceptual model with three AM fungi (Glomus caledonium RIS42 [GC], G. mosseae BEG83 [GM], and Scutellospora calospora WUM12 [SC]) and two soybean varieties (BSR201 and Mandarin). These fungal species have different hyphal lengths and P uptake efficiencies. In order to identify AM fungal species in roots, polymerase chain reaction (PCR)-based techniques were used. Rapid, reliable, and inexpensive DNA extraction techniques were developed from trypan blue-stained mycorrhizal roots. Using PCR of the internal transcribed spacer (ITS) region of ribosomal RNA gene, AM fungal activities (colonization rates) were examined along with plant growth (shoot dry weight) in the treatments with all possible combinations among three AM fungi and two soybean varieties. Although shoot dry weights were not significantly different, colonization rates were different between the two soybean varieties. Our research also showed that mixed planting affected the mycorrhizal colonization, suggesting that the plant community influences AM fungal colonization in roots. AM fungal effects on growth of BSR201 were different among fungal inoculants, but differences were not observed in Mandarin. Scutellospora calospora WUM12 had extremely low colonization with somewhat negative effects in both BSR201 and Mandarin. Our initial conceptual model with three AM fungi did not function as expected because of the low colonization activity of SC and contamination in the GC inoculum. In the GC inoculum, competition between AM fungi might have existed because GC seemed to be excluded from the roots by the contaminant identified as GM by sequence analysis. More research is necessary on the interaction between SC and the host plants to verify the concept of functional complementarity/redundancy between roots and hyphae and preferable host-fungus combinations proposed by Koide (2000).