A novel cationic gemini surfactant (C(12)NDDA) with a spacer containing naphthalene and amides was successfully synthesized. The assembly of C(12)NDDA with -cyclodextrin (-CD) was investigated using various techniques including transmission electron microscopy, proton nuclear magnetic resonance (H-1 NMR), and scanning electron microscopy. Tuning the C(12)NDDA concentration and the C(12)NDDA/-CD molar ratio allowed the production of different assembled aggregate morphologies such as micelles, vesicles, nanowires, nanorods, and hydrogels. Investigation of the inclusion mechanisms of C(12)NDDA and -CD by H-1 NMR revealed that hydrophobic interactions, hydrogen bonding, - stacking, and electrostatic forces play key roles in the assembly process. The antimicrobial activities of the C(12)NDDA/x-CD (x = 0-4) inclusion complexes were tested against Gram-negative bacteria (Escherichia coli and Salmonella) and Gram-positive bacteria (Staphylococcus aureus and Streptococcus), and very low minimum inhibitory concentrations of 0.078-0.31 g mL(-1) were observed. Thus, this newly synthesized gemini surfactant and its inclusion complexes exhibit potential as superior broad-spectrum disinfectants for various biomedical and biotechnological applications.