Sub-nanometric Ni-silicide films are self-assembled by solid phase epitaxy of Ni on a vicinal Si(111) surface. The combination of in situ scanning tunneling microscopy and surface electron diffraction with ex situ X-ray photoelectron spectroscopy allows us to identify -Ni 2 Si as the major constituent crystal phase at the overgrown surface. Then scanning tunneling spectroscopy is employed with ab initio electronic structure calculations, to identify the origins of the surface local density of states and use these 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.