The phthalocyanines are functional materials known as blue-green synthetic dyes and organic semiconductors. P. Linstead and his colleagues succeeded in synthesizing the pigment and reported the molecular composition in 1934. In the same year, J.M Robertson determined the structures of phthalocyanines by X-ray diffraction analysis and revealed the shape to be reminiscent of a four-leaf clover. Thus, phthalocyanines were not only attractive as materials for industrial applications but their characteristic structures also drew the interest of microscopists. Phthalocyanines, on occasion, have been associated historically with electron microscopes, the Field Emission Electron Microscope, FEM, and the Transmission Electron Microscope, TEM. This paper traces the history of the electron microscopes through the studies of these chemical compounds, the phthalocyanines. E. Mueller reported the observation of phthalocyanine molecules using the FEM in 1950. This lens-free electron microscope has a high negative voltage applied to a metal tip encased in an evacuated glass tube. The image that appears on the fluorescent screen emanates from electrons that flow from the tip. For observation of the molecule, they are on the tip. At this case, the FEM became the best microscope in the world. Muller's interpretation of the images, however, faced skepticism based on the experimental and theoretical results of others. Consequently, his research led to a deeper understanding of surface diffusion. J.W. Menter accomplished the direct observation of the crystal lattice of copper and platinum phthalocyanine using the TEM in1956. This microscope employs electron beams and magnetic lenses to magnify the sample. Menter suggested that the intuitive interpretation of lattice image was feasible. While many researchers questioned Menter's idea, several observations of crystal lattices and theoretical works supporting the mechanism of imaging were reported. Fourteen years later, N. Uyeda reported the observation of the hexadecachloro-Cu-phthalocyanine molecule, a species bearing the shape of a four-leaf clover. Finally, Uyeda and his colleague visualized the atoms in the molecule with supporting computer simulations enabling a reliable interpretation of the image in 1979. Through the history of direct observations of the phthalocyanines by the electron microscopes, these molecules became milestones on the road to the atomic resolution.