Au-Cu alloy nanostructures have been synthesized in aqueous phase through co-reduction of HAuCl4.3H2O and CuCl2.2H2O by glucose in presence of hexadecylamine at ∼80 °C. By changing the synthesis conditions, nanostructures of various shapes such as nanowires, multiply twinned tripod, tetrapod, etc were observed. Systematic variation of the synthesis condition not only leads to change in size and particle morphology but also develops various other crystallographic characters in the nanoparticles. Alloying behavior of Au-Cu has been examined through transmission electron microscope operating in its conventional and analytical modes coupled with high resolution phase contrast microscopy. These results suggested that nanostructures are composed of homogeneous Au-Cu alloy. Preferential attachment along {111} and {100} crystallographic facets of Au-Cu alloy nanoparticles led to the formation of nanowires. Multiply twinned branched shape Au-Cu (width of branch ∼30 nm) nanostructures exhibit localized surface plasmon resonance maxima in the near-infrared region. The branched shape Au-Cu alloy nanostructures display better surface enhanced Raman scattering response in the detection of methylene blue as compared to spherical Au nanoparticles.