Anhydrous alkali metal-based manganese oxyiodide nanocrystals have been prepared by reduction of permanganate with LiI in acetone solvent, and their electrochemical properties have been characterized in comparison with hydrous homologues synthesized in aqueous solution. According to X-ray diffraction analysis, all the present manganese oxyiodides show no distinct (hkl) reflections. This indicates the nanocrystalline nature of the materials. Electrochemical measurements reveal that the anhydrous samples have a large initial discharge capacity of >300mAhg−1 at a constant current density of 0.2mAcm−2, which is comparable with the capacities of hydrous samples. Despite the absence of lattice water, however, the manganese oxyiodides suffer from greater capacity loss than the water-containing nanocrystals. According to the differential capacity plot, it is clear that the structural stability of the anhydrous nanocrystals is much poorer than that of the hydrous ones. Given that the iodine species helps to maintain the nanocrystalline nature of the electrode materials, the significant capacity loss for the anhydrous nanocrystals can be explained in terms of structural instability caused by the low concentration of iodine species.