Objective To analyze the microbial community structure， distribution of antibiotic resistance genes and virulence factors in Flammulina velutipes using metagenomic sequencing， and explore its potential food safety risks.Methods Nine retail F. velutipes samples were detected. Total DNA was extracted for metagenomic sequencing， and bioinformatics methods were used to analyze the microbial community composition， antibiotic resistance genes and virulence factors.Results Metagenomic sequencing results indicated that the dominant bacterial phyla in F. velutipes were Pseudomonadota and Bacillota， and the dominant bacterial genera were Ewingella， Leuconostoc， and Pseudomonas. Common foodborne pathogens such as Salmonella enterica， Yersinia enterocolitica， and Listeria monocytogenes were annotated in all nine samples， but with low relative abundances. Microbial diversity was higher in the lower segments than in the upper segments of F. velutipes. While environmental bacteria and pathogens were predominant the upper segments， in contrast， lactic acid bacteria predominated in the lower segments. A total of 2 394 virulence factors were annotated， among them most related to virulence mechanisms such as capsules， flagella， and oligosaccharides. A total of 242 antibiotic resistant genes （ARGs） were annotated， among which rosb （23.68%） and baca （23.41%） had the highest relative abundances， and most ARGs corelated with multidrug resistance mechanism. Species taxonomic annotation was carried out for 68 metagenome-assembled genomes （MAGs）. Of all the MAGs， the dominant phyla were Bacillota and Pseudomonadota， and the dominant genera were Leuconostoc， Pseudomonas， and Lactococcus.Conclusion F. velutipes harbor various foodborne pathogens， virulence factors， and resistance genes， posing significant food safety risks. Enhanced microbial monitoring and corresponding control measures should be implemented throughout the food chain.