There are two types of macrophage in the brain: microglia (which reside in the parenchyma) and non-parenchymal brain-associated macrophages (BAMs). Whether these two populations arise from the same embryonic precursor and/or have distinct lineages is not clear. In-depth spatiotemporal transcriptomic analysis during mouse embryogenesis revealed two distinct macrophage populations detectable at embryonic day 10.5, with one giving rise to macrophages and the other giving rise to BAMs. In addition, TGF-βR was found to control microglia accumulation and identity, whereas this was not the case for BAMs. Together these findings reveal two phenotypically distinct macrophage populations that diverge early in embryogenesis.