Charged nanoscale filaments are well-known in natural systems such as filamentous viruses and the cellular cytoskeleton. The unique properties of these structures have inspired the design of self-assembled nanofibers for applications in regenerative medicine, drug delivery, and catalysis, among others. We report here on an amphiphile of completely different chemistry based on azobenzene and a quaternary ammonium bromide headgroup that self-assembles into highly charged nanofibers in water and orders into two-dimensional crystals. Interestingly small-angle X-ray scattering (SAXS) shows that these fibers of 5.6 nm cross-sectional diameter order into crystalline arrays with remarkably large interfiber spacings of up to 130 nm. Solution concentration and temperature can be adjusted to control the interfiber spacings, and addition of salt destroyed the crystal packing indicating the electrostatic repulsions are necessary for the observed ordering. Our findings here demonstrate the universal nature of this phenomenon in systems of highly charged nanoscale filaments.