Ammonia borane(BH3NH3) is a promising hydrogen storage material because of its high gravimetric (19.6 wt% H2) and volumetric hydrogen density with an accompanying moderate decomposition temperature. Previously reported structures determined by using x-ray and neutron diffraction on hydrides show differences in bond lengths and atomic coordination. Here, the crystal structures of fully and half deuterated ammonia borane were investigated as a function of temperature using powder neutron diffraction. The neutron diffraction patterns show a significant difference due to large difference in the scattering length of D and H. It is evident that an order-disorder phase transition occurs around 225 K for all compounds. At low temperature, the compound crystallizes in the orthorhombic structure with space group Pnm21 and gradually transforms to a high temperature disordered tetragonal structure with space group I/4mm at about 225K. The differential scanning calorimetry studies confirm this phase transformation and also indicate that all compounds melt and decompose at above 370 K. The c cell parameter remains unchanged in the orthorhombic phase from 16 K to 200K and increases liaa nearly above 225K. As the temperature is increased, the BH3-NH3 groups start to reorient along the c axis, and the D/H atoms become disordered, leading to the tetragonal phase transition around 225K.