Abstract:[Background] Heavy metal contamination of agricultural soil is an environmental problem as a result of anthropogenic activities. Cadmium (Cd), one of the most toxic heavy metals, poses health risks to both human being and the ecosystem. [Objective] Aiming at laying a theoretical basis for bioremediation and health risk assessment of Cd, we explored the effect of different levels of Cd on soil (rhizosphere and bulk soil) fungal communities of two oilseed rape species (Brassica napus and B. juncea). [Methods] Through high-throughput sequencing of fungal ribosomal internal transcribed spacer (ITS), the impact of Cd on soil fungal communities of the two species was evaluated. [Results] Cd stress changed the composition and structure of soil fungal communities, but had no significant influence on the alpha diversity of them. Soil Cd concentration and biomass were in significant correlation with the rhizosphere soil fungal communities of the two species and the fungal community of B. juncea bulk soil was significantly correlated with Cd concentration. The molecular ecological networks of soil fungal communities were also affected by Cd pollution, as manifested by the reduced stability and symbiosis of the networks for the fungal communities of B. napus rhizosphere soil, improved stability and attenuated symbiosis of the networks for the fungal communities of B. napus bulk soil, and increased stability and symbiosis of the networks for fungal communities of B. juncea rhizosphere and bulk soil. [Conclusion] Cd pollution influences the indigenous fungal community in soil, which might further change soil ecosystem functions.