H⁺-ATPase rich (HR) cells in zebrafish gill/skin were found to carry out Na⁺ uptake and acid-base regulation through a mechanism similar to that which occurs in mammalian proximal tubular cells. However, the roles of carbonic anhydrases (CAs) in this mechanism in zebrafish HR cells are still unclear. The present study used a functional genomic approach to identify 19 CA isoforms in zebrafish. By screening with whole-mount in situ hybridization, only zca2-like a and zca15a were found to be expressed in specific groups of cells in zebrafish gills/skin, and further analyses by triple in situ hybridization and immunocytochemistry demonstrated specific co-localizations of the 2 zca isoforms in HR cells. Knockdown of zca2-like a caused no change in and knockdown of zca15a caused a decrease in H⁺ activity at the apical surface of HR cells at 24 h post-fertilization (hpf). Later at 96 hpf, both the zca2-like a and zca15a morphants showed increased H⁺ activity and Na⁺ uptake, with concomitant upregulation of znhe3b and downregulation of zatp6voc (H⁺-ATPase C-subunit) expressions. Acclimation to both acidic and low-Na⁺ fresh waters caused upregulation of zca15a expression but did not change the zca2-like a mRNA level in zebrafish gills. These results provide molecular physiological evidence to support the roles of these 2 zCA isoforms in Na⁺ uptake and acid-base regulation mechanisms in zebrafish HR cells.