The bonding nature in the fullerene and Frank-Kasper (FK) polyhedral isomers of M@Si16, M = Ti, Zr, and Hf clusters has been studied using ab initio calculations based on the Gaussian 98 program as well as a ultrasoft pseudopotential plane wave method. The fullerene isomer is found to have double bonds between some Si atoms such that each silicon has two single bonds and a double bond on the cage of these endohedral clusters very similar to C60. There is a mixed sp2-sp3 bonding character between Si atoms and only a small charge transfer from M to the Si cage. The sp2 bonding gives rise to π conjugation. On the other hand in the FK isomer, about three electrons are transferred from M to the Si cage making the bonding nature in this isomer quite different. The ionization potentials of these clusters are large (≈7.5 eV) similar to C60 and the electron affinities are small that make these clusters behave like superatoms.