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This paper presents a real-time energy management algorithm for hybrid ac/dc microgrids involving sustainable energy and hybrid energy storage. This hybrid storage system consists of super capacitors (SC) for ultra-fast load matching beside lithium-ion batteries for relatively long term load buffering. The energy management algorithm aims mainly at managing the energy within the system such that the effect of pulsed (short duration) loads on the power system stability is minimized. Moreover, an average annual saving of around 7% is achieved by shifting loads to off-peak hours. The expected energy needed during a future peak, the time of its occurrence and the current state of charge of both elements of the hybrid storage system are all examples of the inputs to the algorithm. A nonlinear regression technique is used to obtain mathematical models for the uncertain quantities including load and sustainable energy curves. The results show a significant improvement for the system in terms of voltage and power stability by applying the proposed algorithm.