About 1 monolayer of palladium was deposited onto a silicon (111) 7 × 7 surface at a temperature of about 550 K inside an ultrahigh vacuum transmission electron microscope, resulting in formation of Pd2Si nanoislands and a 1 × 1 surface layer. Pd clusters created from an excess of Pd atoms on the 1 × 1 surface layer were directly observed by in situ plan view high-resolution transmission electron microscopy. When an objective aperture was introduced so that electron diffractions less than 0.20 nm were filtered out, the lattice structure of the 1 × 1 surface with 0.33 nm spacing and the Pd clusters with a trimer shape were visualized. It was found that image contrast of the 1 × 1 lattice on the specific height terraces disappeared, and thereby an atomic structure of the Pd clusters was clearly observed. The appearance and disappearance of the 1 × 1 lattice was explained by the effect of the kinematical diffraction. It was identified that a Pd cluster was composed of three Pd atoms without a centered Si atom, which is consistent with the model proposed previously. The feature of the Pd clusters stuck at the surface step was also described.