An efficient and facile procedure is developed for concurrent in situ synthesis and ordered assembly of metal nanoparticles on a periodic two dimensional protein array. The S-layer protein of Bacillus subtilis exhibiting uniform pore size is used as template. Synthesis of gold and silver nanoparticles anchoring on the pores of S-layer is achieved by chemical reduction of respective metal salt laden protein template. Transmission electron microscopy reveals formation of well ordered and separated gold and silver nanoparticles with an average diameter of 6 +/- 1 nm and 4 +/- 1 nm, respectively. The periodic arrangement of nanoparticles is dictated by the native structure of S-layer protein array as the nanoparticle locations are found to be correlated to the nanosized pores of the crystalline S-layer array.