Magnesium is crucial for baculovirus transmission in Culex nigripalpus (Theobald) and Culex quinquefasciatus (Say) larvae. However, the mechanistic role of magnesium in baculovirus transmission is unknown. To investigate the possible role of host response factors in baculovirus transmission, suppression subtractive hybridization was used to identify genes differentially transcribed after magnesium exposure in Cx. quinquefasciatus larvae. Suppression subtractive hybridization was performed in both directions enriching for cDNAs differentially transcribed between a nonmagnesium larval control and magnesium (15 mM MgSO₄) treatment of Cx. quinquefasciatus larvae held for 1 h at 27°C. Clones from differentially transcribed genes were evaluated by sequencing, and relative gene transcription levels were analyzed using quantitative real-time polymerase chain reaction quantitative real-time polymerase chain reaction. Target transcripts up/downregulated by magnesium included Cx. quinquefasciatus troponin C, isocitrate dehydrogenase, allergen, cytochrome b5, chymotrypsinogen, apolipophorins, tryptase gamma, carboxylesterase, prolylcarboxypeptidase, imaginai disc growth factor, aldehyde dehydrogenase, tropomyosin-1, chitotriosidase, heat shock protein 70 B2, inorganic phosphate cotransporter, and many other hypothetical protein genes. Magnesium can alter gene transcription in a vector mosquito population, and understanding this process can provide insight into the mechanistic role of magnesium in baculovirus transmission.