We have studied the formation of Ru nanocluster arrays on several monolayer graphene/Ru Moiré structures with different relative orientations of the graphene and Ru lattices. Experiments and ab initio calculations clearly show that the presence of a graphene/Ru Moiré does not guarantee the ordered adsorption of Ru nanoclusters. The simultaneous deposition of Ru onto coexisting Moirés demonstrates that a structure with aligned graphene and Ru lattices templates the formation of arrays of small Ru clusters with narrow size spread and adsorption exclusively in a single site (the 'low fcc' site). The other Moirés considered here gave rise to substantially larger clusters with broader size distribution and without detectable site selectivity. Calculations explain these findings via the density of states (DOS) at different sites of the graphene/Ru Moiré. The ordered nucleation of many small clusters instead of incorporation of metal atoms into larger ones requires one Moiré site with a large DOS at the Fermi level, so that the binding of metal adatoms to this site is stronger than to competing sites in the Moiré and to existing metal clusters.