Amanita mushrooms are important for both human beings and ecosystems. Some members in this genus are valued edible species, whereas some others are extremely poisonous, and most species are ectomycorrhizal. Significant progress has been made in recent years in our understanding of the diversity, phylogeography and population genetics of Amanita mushrooms. A significant reason for the progress was due to the increasing application of molecular methods in the analyses. In this review, we summarize the researches in the diversity, phylogeography and population genetics of Amanita mushrooms, with the focus on advances over the past 20 years. We also discussed future research directions, including several unresolved topical issues.