DNA is a unique yet useful material to organize nanoscale molecular arrays along the helix axis. In this study, we demonstrate a useful approach for creating molecular arrays inside a double helical DNA. Our approach is based on a host–guest system. Introducing abasic sites into DNA afforded a hydrophobic cavity that serves as a host. A planar aromatic molecule (cationic perylenediimide, PDI) was used as the guest molecule. In an aqueous solution, the PDI molecules tend to aggregate with themselves due to the strong hydrophobicity. In the presence of DNA with the cavity, the binding of the PDI was found to site-specifically occur in the hydrophobic cavity. The unique assembly and arrangement for more than two PDI molecules was achieved by controlling the sizes and positions of the cavities. Our approach would provide a simple and convenient way to construct one-dimensional aromatic arrays in DNA.