We report the X-ray crystal structure of the Au30-xAgx(S-tBu)18 alloy and the effect of the ligand on alloying site preferences. Gold-silver nanoalloys prepared by co-reduction of metal salts are known to have only partial Ag occupancies. Interestingly, Au30-xAgx(S-tBu)18 has 100% Ag occupancy at two sites on the core surface as well as partial Ag occupancies on the surface, capping, and staples sites. The Au30-xAgx(S-tBu)18 (x = 1-5) composition was confirmed by X-ray diffraction and electrospray ionization mass spectrometry studies. Thiolate ligands can be categorized into three classes on the basis of the groups at the α-position as aliphatic, aromatic, and bulky thiols. The effect of the ligand on Ag doping can be clearly seen in the crystal structures of Au36-xAgx(SPh-tBu)24 and Au38-xAgx(SCH2CH2Ph)24 when compared with that of Au30-xAgx(S-tBu)18. Ag is preferentially doped onto the core surface when the ligand is aliphatic, and Ag is doped in both core surface and staple metal sites when the ligand is aromatic or bulky.