An observer-based q-Markov Covariance equivalent realization (QMC) formulation is presented in the paper. It is shown that by inserting an observer in the input–output relationship associated with the dynamical system, a QMC approach can be developed that is applicable to systems with marginally stable or unstable equilibrium points. A system of equations governing all linear state-space realizations, along with the corresponding observers, is derived from matching a set of Markov and Covariance parameters. The solution to this equation system is shown to parameterize all state-space realizations that match the pre-specified correlation functions. Four numerical examples are used to show the utility of the proposed approach. The numerical results show that the observer-based QMC presented in the paper can identify linear SISO and MIMO systems with stable, marginally stable, and unstable characteristics.