Abstract-System identification is a key enabling component for the implementation of quantum technologies, including quantum control. In this paper, we consider the class of passive linear input-output systems, and investigate several basic questions: (1) which parameters can be identified? (2) Given sufficient inputoutput data, how do we reconstruct the system parameters? (3) How can we optimize the estimation precision by preparing appropriate input states and performing measurements on the output? We show that minimal systems can be identified up to a unitary transformation on the modes, and systems satisfying a Hamiltonian connectivity condition called "infecting" are completely identifiable. We propose a frequency domain design based on a Fisher information criterion, for optimizing the estimation precision for coherent input state. As a consequence of the unitarity of the transfer function, we show that the Heisenberg limit with respect to the input energy can be achieved using non-classical input states.Index Terms-Quantum information and control; System identification; Linear systems; Estimation; Stochastic systems I. INTRODUCTION We are currently witnessing the beginning of a quantum engineering revolution [1], marking a shift from "classical devices" which are macroscopic systems described by deterministic or stochastic equations, to "quantum devices" which exploit fundamental properties of quantum mechanics, with applications ranging from computation to secure communication and metrology [2], [3]. While control theory was developed from the need for predictability in the behavior of "classical" dynamical systems, quantum filtering and quantum feedback control theory [4], [5], [6] deal with similar questions in the mathematical framework of quantum dynamical systems.System identification is an essential component of control theory, which deals with the estimation of unknown dynamical parameters of input-output systems; in particular, the identification of linear systems is a well studied subject in classical systems theory [7]. A similar task arises in the quantum setup, and various aspects of the quantum system identification problem have been considered in the recent literature, cf.