•Affiliation networks are integrated with molecular data to examine HIV transmission.•Core-peripheral structure in venue affiliation is associated with HIV transmission.•Popular social venues potentiate sexual affiliation network of minority young MSM.•Molecular and affiliation network approach informs effective network interventions.•A surveillance-research-community partnership is important to address ethical issues. This study investigates the two-mode core-periphery structures of venue affiliation networks of younger Black men who have sex with men (YBMSM). The study examined the association between these structures and HIV phylogenetic clusters, defined as members who share highly similar HIV strains that are regarded as a proxy for sexual affiliation networks. Using data from 114 YBMSM who are living with HIV in two large U.S. cities, our findings indicate that HIV phylogenetic clustering patterns were found to be associated with social clustering patterns whose members share affiliation with core venues that overlap with those of YBMSM. Distinct HIV transmission patterns were found in each city, a finding that can help to inform tailored venue-based and network intervention strategies.