The bacterial pathogenMycobacterium tuberculosisbinds to the C-type lectin DC-SIGN (dendritic cell–specific intercellular adhesion molecule 3-grabbing nonintegrin) on dendritic cells to evade the immune system. While DC-SIGN glycoconjugate ligands are ubiquitous among mycobacterial species, the receptor selectively binds pathogenic species from theM. tuberculosiscomplex (MTBC). Here, we unravel the molecular mechanism behind this intriguing selective recognition by means of a multidisciplinary approach combining single-molecule atomic force microscopy with Förster resonance energy transfer and bioassays. Molecular recognition imaging of mycobacteria demonstrates that the distribution of DC-SIGN ligands markedly differs betweenMycobacterium bovisBacille Calmette-Guérin (BCG) (modelMTBCspecies) andMycobacterium smegmatis(non-MTBCspecies), the ligands being concentrated into dense nanodomains onM. bovisBCG. Upon bacteria-host cell adhesion, ligand nanodomains induce the recruitment and clustering of DC-SIGN. Our study highlights the key role of clustering of both ligands onMTBCspecies and DC-SIGN host receptors in pathogen recognition, a mechanism that might be widespread in host-pathogen interactions.