This paper targets the frequency domain identification of current structural modal properties under earthquake excitation. A new refined Frequency Domain Decomposition (rFDD) algorithm is implemented towards the output-only modal dynamic identification of heavy-damped frame structures, which are subjected to a wide set of strong ground motions. In fact, both seismic excitation and/or high damping values shall not fulfil traditional FDD assumptions. Despite that, with the present rFDD implementation quite limited errors in the modal parameter estimates have been achieved, including for the modal damping ratios (ranging from 1% to 10%). At first, the identification technique is formulated and explored analytically, by proving its potential effectiveness with seismic response input. Then, all strong motion modal parameters are consistently identified. As a fundamental necessary condition, synthetic response signals are adopted. These have been generated prior to dynamic identification from computed numerical seismic responses of a set of shear-type frames. The efficiency of the present original implementation is highlighted, by proving that consistent rFDD modal dynamic identification of structures at seismic input and simultaneous heavy damping looks feasible. Thus, the paper delivers a robust method for inspecting current structural modal properties of frame buildings under earthquake excitation and for observing their possible variation along experienced seismic histories.