Controlling the morphology of magnetic nanoparticles and their spatial arrangement is crucial for manipulating their functional properties. The commonly available inorganic processes for the synthesis of uniform magnetic nanoparticles typically require extreme reaction conditions such as high temperatures or harsh reagents, rendering them unsuitable for making functionalized magnetic nanoparticles with tunable properties controlled by biomolecules. Biomimetic procedures, inspired by the production of uniform magnetite and greigite crystals in magnetotactic bacteria, provide an alternative method, which can allow synthesis and spatial arrangement under ambient conditions. Mms6, an amphiphilic protein found in magnetosome membranes in Magnetospirillum magneticum strain AMB-1, can control the morphology of magnetite nanoparticles, both in vivo and in vitro. In this work, we have demonstrated the patterning of Mms6 and the formation of patterns of magnetic nanoparticles on selective regions of surfaces by directed self-assembly and control over surface chemistry, enabling facile spatial control in applications such as high density data storage and biosensors. Using microcontact printing we have obtained various patterns of 1-octadecane thiol (ODT) and protein resistant poly(ethylene glycol)methyl ether thiol (PEG) layers on gold surfaces. Atomic force microscopy (AFM) and fluorescence microscopy studies show the patterning of Mms6 on the ODT patterns and not on the PEG regions. Magnetic nanoparticles were grown on these surfaces by a co-precipitation method over immobilized protein. AFM and scanning electron microscopy (SEM) results show the localized growth of magnetic nanocrystals selectively on the Mms6 template, which in turn was determined by the ODT regions. Magnetic force measurements were conducted to assess the localization of magnetic nanoparticles on the pattern.