The key challenge in experimental quantum information science is to identify isolated quantum mechanical systems with long coherence times that can be manipulated and coupled together in a scalable fashion. We describe the coherent manipulation of an individual electron spin and nearby individual nuclear spins to create a controllable quantum register. Using optical and microwave radiation to control an electron spin associated with the nitrogen vacancy (NV) color center in diamond, we demonstrated robust initialization of electron and nuclear spin quantum bits (qubits) and transfer of arbitrary quantum states between them at room temperature. Moreover, nuclear spin qubits could be well isolated from the electron spin, even during optical polarization and measurement of the electronic state. Finally, coherent interactions between individual nuclear spin qubits were observed and their excellent coherence properties were demonstrated. These registers can be used as a basis for scalable, optically coupled quantum information systems.