Artificial synthesis of silica under benign conditions is usually achieved by using cationic organic matrices as templates while the anionic analogues have not received enough consideration, albeit they are also functioning in biosilica formation. In this work, we report the design and self-assembly of an anionic peptide amphiphile (I3E) and the use of its self-assemblies as templates to synthesize 1D silica nanostructures with tunable sizes. We show that short I3E readily formed long nanofibrils in aqueous solution via a hierarchical self-assembly process. By using APTES and TEOS as silica precursors, we found that the I3E nanofibrils templated the production of silica nanotubes with a wide size distribution, in which the silica size regulation was achieved by tuning the interactions among the peptide template and silicon species. These results clearly illustrate a facile method for generating silica nanomaterials based on anionic matrices.