Herein, we report the X-ray crystallographic structure of a 38-metal atom Au–Ag alloy nanomolecule. The structure of monometallic Au₃₈(SR)₂₄ consists of 2 central Au atoms and 21 Au atoms forming a bi-icosahedral core protected by 6 dimeric and 3 monomeric units. In Au_38–xAg_x(SR)₂₄,where x ranges from 1 to 5, the silver atoms are selectively incorporated into the Au₂₁ bi-icosahedral core. Within the Au₂₁ core, the silver atoms preferentially occupy nine selected locations: (a) the two vertex edges, three atoms on each edge and six atoms total, and (b) the middle face-shared three-atom ring, adding to a total of nine locations. X-ray crystallography yielded a composition of Au_34.04Ag_3.96(SCH₂CH₂Ph)₂₄. The crystal structure of the alloy nanomolecule can be described in terms of shells as Au₂@Au_17.04Ag_3.96@ 6×[−SR–Au–SR–Au–SR] 3×[−SR–Au–SR−].