The stacking orientation of bilayers determines the polytype of SiC material. So, for the development of polytype heterojunctions a controlled switch from one stacking sequence to another is required. In the present paper it is demonstrated for 4H-SiC and 6H-SiC, that the chemical environment during preparation of the (root3 x root3)R30degrees reconstruction on SiC(0001) influences the bilayer stacking in the topmost surface region. A silicon rich growth environment results in three bilayers in identical orientation at the very surface, which in the case of 4H-SiC corresponds to breaking the bulk stacking sequence. Oxygen rich preparation conditions lead to a reduction to two identically oriented bilayers for both polytypes. The reconstruction geometry of the (root3 x root3)R30degrees phase is independent of the polytype and the terminating stacking sequence of the underlying material. In consequence, the surface stacking and as such the starting point of a polytype heterojunction can be tailored by the chemical potential.