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Remediation of mercury (Hg)-contaminated soil by mycorrhizal technology has drawn increasing attention because of its environmental friendliness. However, the lack of systematic investigations on arbuscular mycorrhizal fungi (AMF) community composition in Hg-polluted soil is an obstacle for AMF biotechnological applications. In this study, the AMF communities within rhizosphere soils from seven sites from three typical Hg mining areas were sequenced using an Illumina MiSeq platform. A total of 297 AMF operational taxonomic units (OTUs) were detected in the Hg mining area, of which Glomeraceae was the dominant family (66.96%, 175 OTUs). AMF diversity was significantly associated with soil total Hg content and water content in the Hg mining area. Soil total Hg showed a negative correlation with AMF richness and diversity. In addition, the soil properties including total nitrogen, available nitrogen, total potassium, total phosphorus, available phosphorus, and pH also affected AMF diversity. Paraglomeraceae was found to be negatively correlated to Hg stress. The wide distribution of Glomeraceae in Hg-contaminated soil makes it a potential candidate for mycorrhizal remediation.