Microglia, the brain-resident immune cells, are critically involved in many physiological and pathological brain processes, including neurodegeneration. Here we characterize microglia morphology and transcriptional programs across ten species spanning more than 450 million years of evolution. We find that microglia express a conserved core gene program of orthologous genes from rodents to humans, including ligands and receptors associated with interactions between glia and neurons. In most species, microglia show a single dominant transcriptional state, whereas human microglia display significant heterogeneity. In addition, we observed notable differences in several gene modules of rodents compared with primate microglia, including complement, phagocytic, and susceptibility genes to neurodegeneration, such as Alzheimer’s and Parkinson’s disease. Our study provides an essential resource of conserved and divergent microglia pathways across evolution, with important implications for future development of microglia-based therapies in humans. Display omitted •Microglia single-cell expression and morphology across 450 million years of evolution•Microglia express a conserved core program, including CNS ligand-receptors pairs•Human microglia show significant heterogeneity in comparison with all mammals•Identification of disease-associated microglia gene expression modules in humans Single-cell sequencing of microglia across evolutionary timescales leads to definition of a conserved core expression program and identification of heterogeneity in human microglia lacking in other species.