<p>The anterior insular cortex (aIC) is involved in multiple neuropsychiatric disorders. Here, using the Cntnap2-deficient autism spectrum disorder (ASD) mouse model and the chronic social defect stress (CSDS)-induced depression mouse model, we show that two subpopulations of microglia in the mouse aIC played differential roles in ASD-like and depression-like behavioral phenotypes differentially. The Cx3cr1⁺ microglia had morphological deficits in the Cntnap2-deficient mice and were involved in social deficits and restricted repetitive behaviors, while the Tmem119⁺ microglia had morphological deficits in the CSDS-induced mice and contributed to impairments in sucrose preference and forced swim performance. Further, we showed that the two subsets of microglia had differential features in morphology, transcriptional profiles, electrophysiological properties, and impacts on synaptic functions. Using proteomic and metabonomic analyses, we identified two secretory factors, Fbl and Hp1bp3, that were crucial for the dysfunctions of the Cx3cr1⁺ and Tmem119⁺ microglia, respectively. Finally, we verified that Fbl and Hp1bp3 played essential roles in the behavioral deficits of the Cntnap2-deficient and the CSDS-induced mice, respectively. Our study can help understand the contribution of microglia and the aIC to neuropsychiatric-like behaviors.</p>