In addition to the classically defined two microglia layers in the plexiform layers, a newly discovered retinal microglia layer is superficially located around the ganglion cell layer (GCL) in contact with the vitreous. We visualized the microglial layers by using CX3CR1-GFP transgenic mice with both healthy and disease conditions. As a disease progresses, each microglial layer gets closer to each retinal capillary plexus, including the superficial, intermediate, and deep capillary plexus, making inter-glial distances more visible. The GCL microglia has two subsets; peripheral (pph) microglia located on the retinal parenchyma and BAM (CNS Border Associated Macrophage) which have a special stretched phenotype only located on the surface of large retinal veins. Frist, in the pph microglia subset, but not in BAM, Galectin-3 and LYVE1 are focally expressed. However, LYVE1 are specifically expressed in the amoeboid or transition forms, except the typical dendritic morphology in the pph microglia. Second, BAM is tightly attached to the surface of the retinal veins and has similar morphology patterns in both the healthy and disease conditions. CD86+ BAM have a longer process which vertically passes the proximal retinal veins. Our data helps decipher the basic anatomy and pathophysiology of the retinal microglia in the GCL.