This paper describes the multi-level reconfigurable hierarchical control of a laboratory prototype Microgrid comprising Photovoltaic (PV), wind turbine, micro-hydro and fuel cell based renewable energy sources. The transient and momentary power back up is incorporated through ultra-capacitor. Prolong power back-up is provided with battery energy storage. The major part of power is generated by renewable energy sources, which produce raw power under varying weather conditions. This may cause disruptive effects such as voltage fluctuations, voltage dips, frequency variation and harmonic distortion on the grid if not properly controlled and coordinated. Issues like intermittent nature of PV and wind sources, significantly different dynamic behavior of various sources and dissimilar generating capacities of sources have an adverse effect on the microgrid operation. For achieving an optimum and reliable performance of the microgrid, a hierarchical control is both necessary and critical. This paper presents a four level 're-configurable' hierarchical control scheme for the microgrid. A notable feature of the proposed architecture is the capability of the resource manager layer to transfer its functionalities to the global microgrid control layer (or vice versa) in the event of emergency. Various aspects related to this kind of microgrid control with relevant analytical and experimental details are presented. © 2013 IEEE.