Arbuscular mycorrhizal fungi (AMF) are ubiquitous, obligatory plant symbionts that have a beneficial influence on plants in contaminated environments. This study focused on evaluating the biomass and biodiversity of the AMF and microbial communities associated with Poa trivialis and Phragmites australis plants sampled at an aged site contaminated with phenol and polynuclear aromatic hydrocarbons (PAHs) and an uncontaminated control site. We analyzed the soil phospholipid fatty acid profile to describe the general structure of microbial communities. PCR-denaturing gradient gel electrophoresis with primers targeting the 18S ribosomal RNA gene was used to characterize the biodiversity of the AMF communities and identify dominant AMF species associated with the host plants in the polluted and control environments. The root mycorrhizal colonization and AMF biomass in the soil were negatively affected by the presence of PAHs and phenol, with no significant differences between the studied plant species, whereas the biodiversity of the AMF communities were influenced by the soil contamination and plant species. Soil contamination was more detrimental to the biodiversity of AMF communities associated with Ph. australis, compared to P. trivialis. Both species favored the development of different AMF species, which might be related to the specific features of their different root systems and soil microbial communities. The contaminated site was dominated by AMF generalists like Funneliformis and Rhizophagus, whereas in the control site Dominikia, Archaeospora, Claroideoglomus, Glomus, and Diversispora were also detected.