The bonding and electronic properties of Inn−, InnSi−, and InnGe− (n = 3–16) clusters have been computationally investigated. An intensive global search for the ground‐state structures of these clusters were conducted using the genetic algorithm coupled with density functional theory (DFT). The ground‐state structures of these clusters have been identified through the comparison between simulated photoelectron spectra (PES) of the found lowest‐energy isomers and the experimentally measured ones. Doping semiconductor atom (Si or Ge) can significantly change the structures of the In clusters in most sizes, and the dopant prefers to be surrounded by In atoms. There are three structural motifs for InnX− (X = Si, Ge, n = 3–16), and the transition occurs at sizes n = 5 and 13. All InnSi− and InnGe− share the same configurations and similar electronic properties except for n = 8. Among all above studied clusters, In13− stands out with the largest vertical detachment energy (VDE), HOMO–LUMO gap, (Eb) and second order energy difference Δ2E due to its closed electronic shell of (1S)2(1P)6(1D)10(2S)2(1F)14(2P)6. Similarly, the neutral In12X (X = Si, Ge) clusters are also identified as superatoms but with electronic configuration of (1S)2(1P)6(2S)2(1D)10(1F)14(2P)6.