The naturally occurring cellulose phase (cellulose I) is crystalline fibrous material that consist of long parallel chains of beta-1,4 linked-D-glucose. Mercerization with solutions of NaOH can produce a phase called cellulose II whose chains are aligned in an antiparallel manner. One of the greatest controversies in the long history of cellulose research has centred on the question of how, during mercerization, crystalline fibers of tightly packed parallel chains that can be thousands of nanometers in length can convert into crystalline fibers of tightly packed antiparallel chains. To answer this question, we have prepared fully deuterated (D) and fully hydrogenated (H) bacterial cellulose. When we use the mixture of D and H cellulose for mercerization, the calculated intensities of reflections are differed by how cellulose chains are packed and aligned in the system; i.e. how D and H is placed either in the unit cell and in the crystal.