This work reports on the preparation of nanoclusters of manganese oxide using biotemplating techniques. Supported lipid bilayers (SLBs) on quartz using cationic lipid [Dioctadecyldimethylammonium bromide (DOMA)] and mixed systems with neutral phospholipids dipalmitoyl phosphatidylcholine (DPPC) and dioleoyl phosphatidylcholine (DOPC) have been used as templates to synthesize these nanoparticles in a waterbased medium at room temperature. The Transmission electron microscopy (TEM) and Scanning electron microscopy (SEM) show manganese oxide nanostructures that are composed of crystals or small clusters in the size range of 20-50 nm in diameter. Small angle XRD showed that template removal through calcining process results in nanostructures of the manganese oxide in sizes from 30 to 50 nm. Using these organized assemblies it is possible to control the nano and mesoscopic morphologies of particles and both rod-like and spherical particles can be synthesized.