Microglia are the principle neuroimmune cells of the brain, having important roles both in brain homeostasis as well as pathological states. Apart from the secretion of pro-inflammatory or anti-inflammatory molecules, they also participate directly at the synaptic level in the remodeling of neuronal circuitries by remodeling mechanisms that include synaptic pruning, synaptic stripping, and synaptic maturation. Thus microglia are known to display diverse roles in different physiological and pathological conditions, largely depending upon the microenvironment they are present in and the context that triggers their activities. One reason for microglia displaying such diverse roles was hypothesized to be the heterogeneous nature of the microglial population, meaning that all microglial cells are not alike and may display differences in their modes of action. For a long time researchers have thus focused on studying this microglial heterogeneity in a number of physiological and pathological states. In 2016, I reported the presence of a novel microglial phenotype in the brain, named the "dark" microglia, while studying microglia-synapse interactions in the contexts of chronic stress, aging, and disease. Using transmission electron microscopy, we described the presence of a microglia-look alike cell, but with a dense cytoplasm and nucleoplasm, as well as loss of nuclear heterochromatin pattern and signs of oxidative stress. We described the increased prevalence of this cell type in mouse models of chronic stress, Alzheimer's disease pathology, aging, and neuron-microglia communication alteration. Using immunoelectron microscopy to study the colocalization of dark microglia with different cell type markers, we further demonstrated the microglial origin of the dark microglia, as well as proposed putative synaptic remodeling roles based on our observations of extensive dark microglia-synapse interactions captured at the ultrastructural level. We have also characterized the presence of dark microglia in postnatal stages of early brain development. Our findings suggested synaptic remodeling roles during normal development, especially in the refinement and maturation of the neuronal circuitry, as well as phagocytosis of apoptotic cells. My thesis thus describes dark microglia as a new microglial phenotype currently seen using electron microscopy (EM) tools. Based on the ultrastructural evidence we have, the dark microglia could represent an important microglial subtype that is primarily involved in synaptic remodeling in an attempt to bring about adaptation of the brain in response to disease or changes in external environment. They could also be an important cell type along with typical microglia that mediates the sculpting and refinement of the neuronal circuitry during early postnatal brain development, when there is an excess of synaptic contacts being formed that need to be pruned out. We therefore highlight the importance of studying the dark microglia, and the need of identifying dark microglia-specific markers to aid with the isolation and further molecular characterization of these cells, to eventually develop therapeutics that utilize the activity of these cells to treat various neurological disorders.