We report a microwave-assisted intramolecular anomeric protection (iMAP) of glucosamine, which facilitates concise transformation of 1,6-anhydroglucosamine into 1,6-anhydrogalactosamine and 1,6-anhydroallosamine. The iMAP simultaneously obviates both the O1 and O6 protection, and the differentiation between O3 and O4 can be well-controlled by the N2 functionality because of the hydrogen bonding between N2 and O4. Epimerization of O4 afforded the galactosamine derivative and that of O3 yielded allosamine.