Septate junctions (SJs) regulate paracellular permeability across invertebrate epithelia. However, little is known about the function of SJ proteins in aquatic invertebrates. In this study, a role for the transmembrane SJ protein gliotactin (Gli) in the osmoregulatory strategies of larval mosquito (Aedes aegypti) was examined. Differences in gli transcript abundance were observed between the midgut, Malpighian tubules, hindgut and anal papillae of A. aegypti, which are epithelia that participate in larval mosquito osmoregulation. Western blotting of Gli revealed its presence in monomer, putative dimer and alternatively processed protein forms in different larval mosquito organs. Gli localized to the entire SJ domain between midgut epithelial cells and showed a discontinuous localization along the plasma membranes of epithelial cells of the rectum as well as the syncytial anal papillae epithelium. In the Malpighian tubules, Gli immunolocalization was confined to SJs between the stellate and principal cells. Rearing larvae in 30% seawater caused an increase in Gli protein abundance in the anterior midgut, Malpighian tubules and hindgut. Transcriptional knockdown of gli using dsRNA reduced Gli protein abundance in the midgut and increased the flux rate of the paracellular permeability marker, polyethylene glycol (molecular weight 400 Da; PEG-400). Data suggest that in larval A. aegypti, Gli participates in the maintenance of salt and water balance and that one role for Gli is to participate in the regulation of paracellular permeability across the midgut of A. aegypti in response to changes in environmental salinity.