Microglia are brain-resident immune cells that contribute to the maintenance of brain homeostasis. In the epileptic brain, microglia show various activation phenotypes depending on the stage of epileptogenesis. Therefore, it remains unclear whether microglial activation acts in a pro-epileptic or anti-epileptic manner. In mesial temporal lobe epilepsy, one of the most common form of epilepsies, microglia exhibit at least two distinct morphologies, amoeboid shape and ramified shape. Amoeboid microglia are often found in sclerotic area, whereas ramified microglia are mainly found in non-sclerotic area;however, it remains unclear whether these structurally distinct microglia share separate roles in the epileptic brain. Here, we review the roles of the two distinct microglial phenotypes, focusing on their pro- and anti-epileptic roles in terms of inflammatory response, regulation of neurogenesis and microglia-neuron interaction.