Sub-nanometric Ni-silicide films were self-assembled by solid phase epitaxy of Ni on a vicinal Si(111) surface. Combination of in-situ scanning tunneling microscopy and surface electron diffraction with ex-situ X-ray photoelectron spectroscopy allowed us to identify Ni2Si as the major constituent crystal phase at the grown surface. We then employed scanning tunneling spectroscopy with ab-initio electronic structure calculations, to obtain and use the surface local density of states as a fingerprint for in-situ phase identification. The above approach enhances the chemical contrast capability of scanning tunneling microscopy, and offers a useful local probe with atomic resolution for in-situ crystal phase identification of ultra-thin surface structures.