Ordered zinc oxide (ZnO) rod arrays with very high orientation were fabricated on Si substrates by using a solution method. The substrate surfaces were functionalized by Self-Assembly Monolayers(SAMs). In the very early growth stage, the oriented ZnO crystals had already grown, which appeared to be themain reason why ZnO nanorods showed very high orientation. The un-dense and un-uniform SAMs provided a surface that was heterogeneous to ZnO nucleation. Consequently, highly oriented ZnO rods were selectively grown on the coin-like SAM-uncovered regions. The route developed here can provide some helpful information to control the nucleation and orientation of ZnO in aqueous solution. Also, the site-selective growth mechanisms can indicate a clue to grow patted highly oriented ZnO nanorod arrays by the organic template.