Macrophages are a highly heterogeneous population of cells, with this diversity stemming in part from the existence of tissue resident populations and an ability to adopt a variety of activation states in response to stimuli. Drosophila blood cells (hemocytes) are dominated by a lineage of cells considered to be the functional equivalents of mammalian macrophages (plasmatocytes). Until very recently plasmatocytes were thought to be a homogeneous population. Here, we identify enhancer elements that label subpopulations of plasmatocytes, which vary in abundance across the lifecourse of the fly. We demonstrate that these plasmatocyte subpopulations behave in a functionally-distinct manner when compared to the overall population, including more potent migratory responses to injury and decreased clearance of apoptotic cells within the developing embryo. Additionally, these subpopulations display differential localisation and dynamics in pupae and adults, hinting at the presence of tissue-resident macrophages in the fly. Our enhancer analysis also allows us to identify novel candidate genes involved in plasmatocyte behaviour in vivo. Misexpression of one such enhancer-linked gene (calnexin14D) in all plasmatocytes improves wound responses, causing the overall population to behave more like the subpopulation marked by the calnexin14D-associated enhancer. Finally, we show that, we are able to modulate the number of cells within some subpopulations via exposure to increased levels of apoptotic cell death, thereby decreasing the number of plasmatocytes within more wound-responsive subpopulations. Taken together our data demonstrates the existence of macrophage heterogeneity in Drosophila and identifies mechanisms involved in the specification and function of these plasmatocyte subpopulations. Furthermore, this work identifies key molecular tools with which Drosophila can be used as a highly genetically-tractable, in vivo system to study the biology of macrophage heterogeneity.