The study investigates the transcriptional mechanisms that specify human microglia phenotypes, focusing on the environment-dependent changes in gene expression. Human microglia were isolated from surgically resected brain tissue and compared to those cultured in vitro. The transition to an in vitro environment resulted in rapid and extensive downregulation of microglia-specific genes, similar to what is observed in mouse macrophages following migration into the fetal brain. These changes are associated with altered expression of genes linked to neurodegenerative and behavioral diseases and non-coding risk variants. The study also examines the enhancer landscapes and epigenetic features of human microglia, revealing conserved and species-specific differences. Overall, the findings highlight an environment-dependent transcriptional network that specifies microglia-specific gene expression programs and provide insights into the roles of microglia in human disease.The study investigates the transcriptional mechanisms that specify human microglia phenotypes, focusing on the environment-dependent changes in gene expression. Human microglia were isolated from surgically resected brain tissue and compared to those cultured in vitro. The transition to an in vitro environment resulted in rapid and extensive downregulation of microglia-specific genes, similar to what is observed in mouse macrophages following migration into the fetal brain. These changes are associated with altered expression of genes linked to neurodegenerative and behavioral diseases and non-coding risk variants. The study also examines the enhancer landscapes and epigenetic features of human microglia, revealing conserved and species-specific differences. Overall, the findings highlight an environment-dependent transcriptional network that specifies microglia-specific gene expression programs and provide insights into the roles of microglia in human disease.