The objective of the present study was to examine the branchial distribution of the recently identified rainbow trout cytoplasmic carbonic anhydrase isoform (tCAc) and to investigate its role in the regulation of acid-base disturbances in rainbow trout (Oncorhynchus mykiss). In situ hybridization using an oligonucleotide probe specific to tCAc revealed tCAc mRNA expression in both pavement cells and mitochondria-rich cells (chloride cells). Similarly, using a homologous polyclonal antibody, tCAc immunoreactivity was localized to pavement cells and mitochondria-rich cells in the interlamellar region and along the lamellae of the gills. Exposure of rainbow trout to hypercarbia (approximately 0.8% CO2) for 24 h resulted in significant increases in tCAc mRNA expression (approximately 20-fold; quantified by real-time PCR) and protein levels (approximately 1.3-fold; quantified by western analysis) but not enzyme activity (assessed on crude gill homogenates using the delta-pH CA assay). Inhibition of branchial CA activity in vivo using acetazolamide reduced branchial net acid excretion significantly by 20%. This effect was enhanced to a 36% reduction in branchial net acid excretion by subjecting the trout to hypercarbia (approximately 0.8% CO2) for 10 h prior to acetazolamide injection, an exposure that significantly increased branchial net acid excretion. The results of the present study support the widely held premise that branchial intracellular CA activity (tCAc) plays a key role in regulating acid-base balance in freshwater teleost fish.