Process for producing a hybrid substrate, in which: a) a first substrate (10, 110, 210) is prepared comprising a mixed layer that lies alongside a continuous, electrically insulating underlying layer and that is formed from single-crystal first zones (12A, 112A, 212A) made of at least one crystalline first material, and adjacent second zones made of an amorphous second material (12B, 112B, 212B), the second zones forming at least one portion of the free surface of this first substrate; b) a second substrate (20, 120, 220), comprising on its surface a reference layer having a given crystal orientation, is bonded to this first substrate by molecular bonding in at least the amorphous zones; c) a heat treatment is carried out on the mixed layer, said heat treatment being suitable for causing at least one portion of the amorphous zones (12B, 112B, 212B) to recrystallize, in the solid state, with the crystal orientation of the reference layer (20, 120, 220), this reference layer acting as a crystallization seed across the bonding interface; and d) the reference layer of the second substrate and the at least partially recrystallized zones of the first substrate are separated, characterized in that • the molecular bonding is hydrophobic; • before step b), the process comprises roughening at least one of the faces, of the first or second substrate, intended to be bonded by molecular bonding, carried out so that the roughness obtained is comprised between 0.1 nm and 1 nm RMS, thereby allowing the bonding energy to be decreased despite the consolidation that normally takes place because of the heat treatment in step c); and • the separation takes place in a fragile zone consisting of the molecular bonding interface between the first and second substrates. a) a first substrate (10, 110, 210) is prepared comprising a mixed layer that lies alongside a continuous, electrically insulating underlying layer and that is formed from single-crystal first zones (12A, 112A, 212A) made of at least one crystalline first material, and adjacent second zones made of an amorphous second material (12B, 112B, 212B), the second zones forming at least one portion of the free surface of this first substrate; b) a second substrate (20, 120, 220), comprising on its surface a reference layer having a given crystal orientation, is bonded to this first substrate by molecular bonding in at least the amorphous zones; c) a heat treatment is carried out on the mixed layer, said heat treatment being suitable for causing at least one portion of the amorphous zones (12B, 112B, 212B) to recrystallize, in the solid state, with the crystal orientation of the reference layer (20, 120, 220), this reference layer acting as a crystallization seed across the bonding interface; and d) the reference layer of the second substrate and the at least partially recrystallized zones of the first substrate are separated, • the molecular bonding is hydrophobic; • before step b), the process comprises roughening at least one of the faces, of the first or second substrate, intended to be bonded by molecular bonding, carried out so that the roughness obtained is comprised between 0.1 nm and 1 nm RMS, thereby allowing the bonding energy to be decreased despite the consolidation that normally takes place because of the heat treatment in step c); and • the separation takes place in a fragile zone consisting of the molecular bonding interface between the first and second substrates.