In this paper, a flow variance based structural damage identification method is introduced. It is a practical implementation of phase space warping concept as applied to damage identification. A coupled dynamical system is considered where a slow-time damage process causes drifts in the parameters of fast-time system describing measurable response of a structure. The method is based on the hypothesis that the distribution function of the fast-time trajectory is a function of damage state. In this method, estimated local expectation of trajectory in its phase space is used as a damage tracking feature vector. After the feature vectors are constructed, damage identification is realized by smooth orthogonal decomposition. Data processing time requirements of the flow variance based approach decrease by about 2 orders-of-magnitude compared with the phase space warping based method. A common form of the feature vectors is also discussed.