We provide a general framework for the identification of open quantum systems. By looking at the input-output behavior, we try to identify the system inside a black box in which some Markovian time-evolution takes place. Due to the generally irreversible nature of the dynamics, it is difficult to assure full controllability over the system. Still, we show that the system is identifiable up to similarity under a certain rank condition. The framework also covers situations relevant to standard quantum process tomography, where we do not have enough control over the system but have a tomographically complete set of initial states and observables. Remarkably, the similarity cannot in general be reduced to unitarity even for unitary systems, and the spectra of Hamiltonians are not identifiable without additional knowledge.