Bacterial flagellum is a protein nanotube that is helically self-assembled from thousands of a protein subunit called flagellin. The solvent-exposed domain of each flagellin on the flagella is genetically modifiable, in that a foreign peptide can be genetically inserted into this domain, leading to the high-density display of this foreign peptide on the surface of flagella. In this work, wild-type and genetically engineered flagella (inner diameter of ∼2 nm and outer diameter of ∼14 nm) detached from the surface of Salmonella bacterial cells are used as templates to site-specifically form silica sheaths on the flagellar surface, resulting in the formation of double-layered silica/flagella nanotubes. The flagella templates inside the silica/flagella nanotubes can be removed to obtain silica nanotubes by calcining the nanotubes at high temperature (550°C). Further calcination of the silica nanotubes at a higher temperature (800 °C) leads to the formation of a periodic nanohole array along the silica fibers with a center-to-center nanohole spacing of ∼79 nm. It is demonstrated that the double-layered silica-flagella nanotubes can be used for selective CdTe quantum dot uptake into the inner channels or selective Au nanoparticle coating on the outer wall of the nanotubes due to the different chemistry between inner flagellum core (protein) and outer silica wall of the nanotubes. It is also found that flagella displaying different peptides result in different morphologies of the silica nanotubes. This work suggests that the monodisperse diameter and genetically tunable surface chemistry of the flagella can be exploited for the fabrication of silica nanotubes with uniform diameter and controllable morphologies as well as silica nanofibers decorated with periodic nanohole arrays.