We investigate atomic layer deposition (ALD) of metal oxide on pristine and functionalized graphene. On pristine graphene, ALD coating can only actively grow on edges and defect sites, where dangling bonds or surface groups react with ALD precursors. This affords a simple method to decorate and probe single defect sites in graphene planes. We used perylene tetracarboxylic acid (PTCA) to functionalize the graphene surface and selectively introduced densely packed surface groups on graphene. Uniform ultrathin ALD coating on PTCA graphene was achieved over a large area. The functionalization method could be used to integrate ultrathin high-k dielectrics in future graphene electronics.