In this study the initial stage nucleation and growth of Ni silicide on (001) Si by evaporation and furnace annealing have been investigated by transmission electron microscopy. The pressure was $10^{-6}$ Torr during evaporation and annealing. And the annealing temperature to produce $NiSi_2;was;800^{circ}C$. From the evaporated film, $NiSi_2$ nucleus has grown into Si substrate with an epitaxial orientation relationship. Interfaces between $NiSi_2$ and Si were A-type {111} interfaces and {100} $NiSi_2$ interfaces were also observed at the initial stage of nucleation. Ni silicide grew into Si substrate, but the nucleus partly grew into the evaporated film, with no facets, from the nuclei in the Si substrate. $NiSi_2$ nucleus with (111) habit planes was also observed.