Gold nanoparticles protected by a binary mixture of thiolate molecules have a ligand shell that can spontaneously separate into nanoscale domains. Complex morphologies arise in such ligand shells, including striped, patchy, and Janus domains. Characterization of these morphologies remains a challenge. Scanning tunneling microscopy (STM) imaging has been one of the key approaches to determine these structures, yet the imaging of nanoparticles' surfaces faces difficulty stemming from steep surface curvature, complex molecular structures, and the possibility of imaging artifacts in the same size range. Images obtained to date have lacked molecular resolution, and only domains have been resolved. There is a clear need for images that resolve the molecular arrangement that leads to domain formation on the ligand shell of these particles. Herein we report an advance in the STM imaging of gold nanoparticles, revealing some of the molecules that constitute the domains in striped and Janus gold nanoparticles. We analyze the images to determine molecular arrangements on parts of the particles, highlight molecular “defects” present in the ligand shell, show persistence of the features across subsequent images, and observe the transition from quasi-molecular to domain resolution. The ability to resolve single molecules in the ligand shell of nanoparticles could lead to a more comprehensive understanding of the role of the ligand structure in determining the properties of mixed-monolayer-protected gold nanoparticles.