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Objective: To explore the clustering of HIV infected men having sex with men (MSM) using social network approach in conjunction with the phylogenetic relationship of the virus strains. Design: An exploratory study incorporating social network and phylogenetic analysis. Methods: Recently diagnosed HIV-infected MSM attending one major HIV specialist clinic in Hong Kong were recruited in the study involving the administration of a selfadministered questionnaire on behaviours and partnership patterns using a Likert Scale, the results of which were assessed using social network analysis and in context of the phylogenetic analysis from sequencing the HIV-1 pol gene, as part of the clinical investigation for genotypic resistance. Clusters were defined using social and molecular methods. Results: An ‘Internet-centred’ cluster and ‘Sauna-centred’ cluster could be delineated using correspondence analysis and network diagrams. The main distinguishing features of MSM in the ‘Internet-centred’ social cluster were: younger age, higher education level, and multiple partner types. Three genetic clusters could be identified in the phylogenetic tree, two of which associated with Internet use and one with sauna for sex partnership. There were partial overlaps between social and genetic clusters. Characteristically, the virus strains in sauna users were more disperse compared with the closely knit configuration of those using Internet. Conclusion: The principle of the duality of place and person can be strategically applied in epidemiologic investigation. The characterization of MSM cluster using anonymized network data provides a potentially powerful tool for informing public health intervention.