Cytoplasmic dynein is microtubule-based motor protein utilizing the energy from ATP hydrolysis and plays fundamental roles in various cellular activities including mitosis, vesicle transport and cell migration. Cytoplasmic dynein is a huge protein complex consisting of the head domain and the tail domain. The head domain consists of six AAA modules and a stalk. So far, many studies have investigated about the head domain, because it contains ATP hydrolysis and motor activities. On the other hand, the tail domain consists of N-terminal third of heavy chains (HC), intermediate chains (IC), light intermediate chains (LIC), and light chains (LC). Although the tail domain is implicated in binding of cargos and some of dynein binding proteins which control motor activities of dynein, for example dynactin, the detailed molecular architecture of the tail domain remains to be unveiled. In this study, we observed cytoplasmic dynein molecules with or without polyhistidine tag (His-tag) by transmission electron microscopy (TEM), performed single particle image analysis and obtained the averaged image of the tail domain. Using nickel nitrilotriacetic acid (Ni-NTA) conjugated gold nanoparticles to label His-tag of recombinant proteins, we identified the positions of N-terminus and C-terminus of IC and determined its orientation in the tail domain. Furthermore, we identified the position of C-terminus of LIC relative to IC. Based on our observations, we propose a new model of the architecture of the dynein tail domain which differs from currently advocating model.