In situ hybridization was performed on sections of rainbow trout (Oncorhynchus mykiss) gill tissue using oligonucleotide probes complementary to the mRNA of the 3 1-kilodalton subunit of the bovine renal V-type H+-ATPase or rat kidney Band 3 anion exchanger (C1-IHCO, exchanger). This was conducted in conjunction with measurements of whole-body net acid fluxes and blood acid-base status during imposed conditions of respiratory acidosis (external hypercapnia) or metabolic alkalosis (NaHCO, infusion). A positive hybridization signal for the H+-ATPase mRNA was localized predominantly in lamellar epithelial cells and was less apparent in cells associated with the filament or interlamellar regioqs. The Hf -ATPase hybridization signal was enhanced during hypercapnic acidosis concurrently with a marked increase in whole-body net acid excretion. A positive hybridization signal for the C1-IHCOj exchanger mRNA was observed in epithelial cells on both the filament and lamella. During metabolic alkalosis induced by intra-arterial infusion of NaHCO,, there was a marked increase in the C1-/HCO; exchanger mRNA hybridization signal in cells on both the filament and lamella that occurred concurrently with a decrease in net acid excretion. The results of this study support the existence of a V-type Hf -ATPase and a Cl-/HCO; exchanger in rainbow trout gill epithelial cells and demonstrate that alterations in gene expression for the pump-exchanger may be a significant mechanism underlying the altered rates of net acid equivalent excretion during acid-base disturbances.