This is the author accepted manuscript. The final version is available from EDP Sciences via the DOI in this record.Aims. 51 Oph is one of the few young Be stars displaying a strong CO overtone emission at 2.3 microns in addition to the near infrared excess commonly observed in this type of stars. In this paper we first aim to locate the CO bandheads emitting region. Then, we compare its position with respect to the region emitting the near infrared continuum. Methods. We have observed 51 Oph with AMBER in low spectral resolution (R=35), and in medium spectral resolution (R=1500) centered on the CO bandheads. Results. The medium resolution AMBER observations clearly resolve the CO bandheads. Both the CO bandheads and continuum emissions are spatially resolved by the interferometer. Using simple analytical ring models to interpret the measured visibilities, we find that the CO bandheads emission region is compact, located at 0.150.07 −0.04AU from the star, and that the adjacent continuum is coming from a region further away (0.250.06 −0.03AU). These results confirm the commonly invoked scenario in which the CO bandheads originate in a dust free hot gaseous disk. Furthermore, the continuum emitting region is closer to the star than the dust sublimation radius (by at least a factor two) and we suggest that hot gas inside the dust sublimation radius significantly contributes to the observed 2 µm continuum emissionThis project was partially supported by the PRIN INAF 2006 grant ”From Disks to Planetary Systems”. At LAOG E.T. is supported by a postdoc grant from CNRS/INSU, France. This research is supported by Agence Nationale de la Recherche (ANR) of France through contract ANR-07-BLAN-0221 and by Programme National de Physique Stellaire (PNPS) of CNRS/INSU, France.A.N. and L.T. were partially supported by the INAF 2005 grant “Interferometria infrarossa: ottimizzazione di osservazioni astrofisich” and by the INAF 2006 grant “From Disks to Planetary Systems”.