Soil type and domestication are the main factors that contribute to the determination of root-associated bacterial communities in soybean; however, to what extent these factors influence root-associated fungal communities remains unclear. Here, we grew wild soybean (Glycine soja) and cultivated soybean (Glycine max) in three soil suspensions (black, red and saline-sodic soil) and analyzed the soybean rhizosphere fungal internal transcribed spacer 1 (ITS1) region by high-throughput sequencing technology. The results showed that the fungal communities had significantly different richness and alpha-diversity indexes in the three soil suspensions; however, there was no marked difference in the rhizosphere fungal communities between the two wild and cultivated soybean varieties. Furthermore, soil type was a main factor in determining the distribution of arbuscular mycorrhizal fungi (AMF; Paraglomus and Rhizophagus) and soybean pathogenic fungi (Fusarium and Rhizoctonia). In addition, the abundant rhizosphere fungi from wild soybean exhibited diverse potential functions, while the functions of rhizosphere fungi from cultivated soybean were mainly related to plant nutrient uptake. The diversity and structure of the soybean rhizosphere fungal communities were mainly affected by soil type rather than soybean variety, and domestication caused wild and cultivated soybeans to recruit different rhizosphere fungi. Accordingly, a thorough understanding of soybean fungal communities and their influencing factors is important for improving the health and harvest of soybean.