The V-ATPase B subunit cDNA isolated from the midgut and Malpighian tubules of Culex quinquefasciatus larvae has a 1476 bp ORF encoding a 492 amino acids protein with a predicted mass of 54.8 kDa. Northern blot analysis reveals the presence of 1.8 and 4.2 kb transcripts in larvae and a 3.0 kb transcript in pupae. A single 57 kDa protein band is detected in immunoblot analysis of protein extracts from C. quinquefasciatus and A. aegypti larvae. Using antibodies to the B subunits we demonstrate high-level expression of these subunits in ion-transporting cells of caeca and anterior midgut, and in Malpighian tubules and rectum. High V-ATPase expression was also observed in the larval salivary glands, central nervous system neurophile, the thoracic endocrine complex and in imaginal discs.