In this paper, we address the robust dynamic output feedback control problem of continuous time active fault tolerant control system with Markovian parameters (AFTCSMP) subject to structured parameter uncertainties. We will first derive a necessary and sufficient condition for the robust exponential stability in the mean square of the uncertain AFTCSMP under a dynamic output feedback control, in terms of coupled matrix inequalities, and then we will give an LMI (linear matrix inequalities) characterization of dynamical compensators that robustly stabilize the closed-loop system in the mean square sense