Objective:To investigate the molecular epidemiological characteristics of HIV-1 infection among men who have sex with men (MSM) in Jiaxing city, and provide methods and ideas for the prevention and control of HIV-1 infection.Methods:This study retrospectively collected the blood samples from all newly reported cases of HIV-1 infection among MSM without antiviral treatment from 2020 to 2022. HIV-1 pol genes in the blood samples were amplified and sequenced. MEGA v6.0 software was used to analyze nucleic acid sequences. A phylogenetic tree was constructed to analyze HIV-1 subtypes. The calibrated population resistance program (CPR) was used to detect drug-resistant mutations. After calculating the genetic distance between gene sequences, molecular transmission networks were constructed using Cytoscape v3.6.0 software. Results:A total of nine genetic subtypes were identified, with CRF07_BC (43.3%) and CRF01_AE (36.9%) accounting for the most. The recombinant forms that were not clustered with the reference subtype accounted for 5.0%. Drug-resistant mutations were identified in 21 cases (7.0%), and the mutation rates among strains of CRF07_BC and CRF01_AE subtypes were 8.2% and 7.8%, respectively. The detection rates of drug-resistant mutations to protease inhibitors, nucleoside reverse transcriptase inhibitors and non-nucleoside reverse transcriptase inhibitors were 1.7%, 0.7% and 4.7%, respectively. The optimal genetic distance threshold of the molecular network was 0.018. At this genetic distance, the molecular network access rate was 43.3%, and 38 molecular clusters (ranging from 2 to 26 nodes per cluster) were included. Cases with ≥6 homosexual partners and a degree value of ≥4 were more likely to access the active molecular cluster. The population of high-risk transmission cases with TNS>0.75 were mainly nonlocal residents and commercial service providers. The recombinant forms showed high similarity in sequences with the strains from other provinces.Conclusions:The distribution of HIV-1 subtypes in MSM in Jiaxing city was complex. Given the increasing detection rate of recombinant forms, the high transmission rate of drug-resistant mutations, and the active molecular clusters and high-risk transmission clusters mainly detected in nonlocal residents and commercial service providers, strengthened surveillance and intervention are needed.