Thiolato-protected gold nanoclusters have acquired wide applications; however, on the fundamental science end there is still a lack of deep understanding of their high stability. Recent success in transforming the highly robust biicosahedral Au-38(SCH2CH2Ph)(24) nanocluster into an extremely stable tetrahedral Au-36(SPh-Bu-t)(24) nanocluster raises an important question: Is the transformation due to the bulkiness effect of SPh-Bu-t or the electronic conjugation effect of the aromatic ligand as opposed to the nonaromatic SCH2CH2Ph? Toward this goal, we report our success in the crystallization of a nonaromatic thiolato-protected Au-36(SC5H9)(24) nanocluster (where, SC5H9 = cyclopentanethiolato). Comparison of Au-36(SC5H9)(24) with the aromatic thiolato-protected Au-36(SPh-Bu-t)(24) nanocluster rules out the thought that the face-centered cubic, tetrahedral structure of Au-36(SPh-Bu-t)(24) is dictated by the aromatic ligand; it also reveals that the electronic conjugation effect in aromatic ligand makes the S-C bond shorter and stronger, and this affects the S-Au bonds, resulting in a larger separation between the staple motifs and the inner Au-28 kernel. Overall, this work sheds some light on the major question of the determining the cluster size and structure. specific roles of thiol ligand in determining the cluster size and structure.