Entomopathogenic fungi serve as eco-friendly alternatives to chemical pesticides. In this study, we investigate the interactions between mosquitoes and Metarhizium anisopliae JEF-157, which showed high insecticidal activity against mosquitoes, by RNA-seq analysis. RNA from mosquitoes was extracted at the median lethal time to identify changes in gene expression. The results showed 580 genes were up-regulated, while 336 genes were down-regulated in fungal treated mosquitoes. Up-regulated genes were related to metabolic and cellular processes such as cytochrome P450, DNA replication, and apoptosis. Down-regulated genes were involved in metabolism pathways such as lysosome, starch and sucrose metabolism, and fatty acid biosynthesis. These results are crucial for elucidating the mechanisms of fungal invasion and interaction in insects, providing insights for future pest management strategies.