Nanotechnology is a cutting edge investigation area that has come out with new and unlimited applications. The recent explosion of research in this field, combined with important discoveries in molecular biology have created a new interest in bio-nanorobotic communication. This thesis provides a general theoretical understanding of nanonetworks and their multiple possibilities. It describes some basic concepts of architectures that compose nanotechnology topologies, as well as possible designs for the tiny nanonetwork components, the nanomachines. The thesis also reviews some promising methods proposed for communicating and coordinating in these nanonetworks. Molecular communication applied to nanonetworks presents indeed extremely appealing features in terms of energy consumption, reliability and robustness. Nevertheless, it remains to understand the impact of the extremely slow propagation of molecules and the highly variable environments. As a totally unexplored research area, it is important to establish thorough theoretical framework so that the applications and possible solutions can be validated. It is clear that many issues still need to be addressed in order to understand the limiting performance of information communications among nano-scale devices and design optimal and quasi-optimal encoding/decoding strategies. Such issues are believed to be of key relevance for allowing nanotechnologies display their full potential.