Heptamethinecyanine J-aggregates display sharp, intense fluorescence emission making them attractive candidates for developing a variety of chem-bio-sensing applications. They have been immobilized on planar thiol-covered Au surfaces and thiol-capped Au nanoparticles by weak molecular interactions. In this work the self-assembly of novel thiolated cyanine (CNN) on Au(111) and citrate-capped AuNPs from solutions containing monomers and J-aggregates has been studied by using STM, XPS, PM-IRRAS, electrochemical techniques and Raman spectroscopy. Data show that CNN species adsorb on the Au surfaces by forming thiolate-Au bonds. We found that the J-aggregates are preferentially adsorbed on the Au(111) surface directly from the solution while adsorbed CNN monomers cannot organize into aggregates on the substrate surface. These results indicate that the CNN-Au interaction is not able to disorganize the large J-aggregates stabilized by π-π stacking to optimize the S-Au binding site but it is strong enough to hinder the π-π stacking when CNNs are chemisorbed as monomers. The optical properties of the J-aggregates remain active after adsorption. The possibility of covalently bonding CNN J-aggregates to Au planar surfaces and Au nanoparticles controlling the J-aggregate/Au distance opens a new path regarding their improved stability and the wide range of biological applications of both CNN and AuNP biocompatible systems.