The fungus Floccularia luteovirens is mainly distributed in the alpine meadows of the Qinghai–Tibet plateau. Its fruit bodies tend to form fairy rings with a visible stimulating zone. Our previous studies have investigated the large-scale genetic structure among wild populations of F. luteovirens, but the mechanisms underlying the current genotype distribution pattern remain unknown. The balance between sexual and asexual reproduction affects the establishment and structure of populations. Measuring genet size and density is an effective approach to investigating the reproduction strategies of this species. In the current study, 234 fruit bodies and 79 soil samples were collected from three sampling sites over 3y, revealing that F. luteovirens exhibits relatively large genets. Very few new genets were detected over the 3y, illustrating that this species relies more on vegetative growth and can persist for long periods underground as mycelia. Moreover, the underground genet data showed a close relationship with the above-ground genet data. Our study found limited fine-scale gene flow, contrary to our previous large-scale genetic study of F. luteovirens, the present study found limited fine-scale gene flow of this species. The commercial trade of F. luteovirens fruit bodies by humans probably enhances the gene flow over QTP.