To ensure proper timing of chromosome duplication during the cell cycle, bacteria must carefully regulate the activity of initiator protein DnaA and its interactions with the unique replication origin oriC. Although several protein regulators of DnaA are known, recent evidence suggests that DnaA recognition sites, in multiple genomic locations, also play an important role in controlling assembly of pre-replicative complexes. In oriC, closely spaced high- and low-affinity recognition sites direct DnaA-DnaA interactions and couple complex assembly to the availability of active DnaA-ATP. Additional recognition sites at loci distant from oriC modulate DnaA-ATP availability by repressing new synthesis, recharging inactive DnaA-ADP, or titrating DnaA. Relying on genomic DnaA binding sites, as well as protein regulators, to control DnaA function appears to provide the best combination of high precision and dynamic regulation necessary to couple DNA replication with cell growth over a range of nutritional conditions.