Macrophages reside in essentially all tissues of the body and play key roles in innate and adaptive immune responses. Distinct populations of tissue macrophages also acquire context-specific functions that are important for normal tissue homeostasis. To investigate mechanisms responsible for tissue-specific functions, we analyzed the transcriptomes and enhancer landscapes of brain microglia and resident macrophages of the peritoneal cavity. In addition, we exploited natural genetic variation as a genome-wide “mutagenesis” strategy to identify DNA recognition motifs for transcription factors that promote common or subset-specific binding of the macrophage lineage-determining factor PU.1. We find that distinct tissue environments drive divergent programs of gene expression by differentially activating a common enhancer repertoire and by inducing the expression of divergent secondary transcription factors that collaborate with PU.1 to establish tissue-specific enhancers. These findings provide insights into molecular mechanisms by which tissue environment influences macrophage phenotypes that are likely to be broadly applicable to other cell types. Display omitted •Tissue environment is a major determinant of resident macrophage gene expression•Environment selectively activates common enhancers in different macrophage subsets•Environment primes and activates subset-specific enhancers and super-enhancers•Genetic variation enables discovery of subset-specific transcription factors Genomic and genetic approaches reveal that distinct environmental factors activate shared enhancers and induce expression of population-restricted transcription factors that prime and activate subset-specific enhancers in tissue macrophages.