As immune sentinels of the central nervous system (CNS), microglia not only respond rapidly to pathological conditions but also contribute to homeostasis in the healthy brain. In contrast to other populations of the myeloid lineage, adult microglia derive from primitive myeloid precursors that arise in the yolk sac early during embryonic development, after which they self-maintain locally and independently of blood-borne myeloid precursors. Under neuro-inflammatory conditions such as experimental autoimmune encephalomyelitis, circulating monocytes invade the CNS parenchyma where they further differentiate into macrophages or inflammatory dendritic cells. Often it is difficult to delineate resident microglia from infiltrating myeloid cells using currently known markers. Here, we will discuss the current means to reliably distinguish between these populations, and which recent advances have helped to make clear definitions between phenotypically similar, yet functionally diverse myeloid cell types.