H(+)-ATPase-rich (HR) cells in zebrafish are known to be involved in acid secretion and Na(+) uptake mechanisms in zebrafish gills/skin; however, little is known about how HR cells are functionally regulated. In the present work, we studied the roles of Drosophila glial cell missing (gcm), a cell fate-related transcription factor, in the differentiation and functional regulation of zebrafish HR cells. Zebrafish gcm2 (zgcm2) was found to begin expression in zebrafish embryos at 10 h postfertilization (hpf), and to be extensively expressed in gills but only mildly so in eyes, heart, muscles, and testes. By whole mount in situ hybridization, zgcm2 mRNA signals were found in a group of cells on the zebrafish yolk sac surface initially in the tail bud stage (10 hpf); they had disappeared at 36 hpf and thereafter appeared again in the gill region from 48 hpf. Double fluorescence in situ hybridization further demonstrated specific colocalization of zgcm2 mRNA in HR cells in zebrafish embryos. Knockdown of zgcm2 with a specific morpholino oligonucleotide caused the complete disappearance of HR cells with a concomitant decrease in H(+) activity at the apical surface of HR cells, but it did not affect the occurrence of Na(+)-K(+)-ATPase-rich cells. A decrease in the H(+)-ATPase subunit A (zatp6v1a) expression and no change in zgcm2 expression in zebrafish gills were seen from 12 h to 3 days after transfer to acidic fresh water, but a compensatory stimulation in the expressions of both genes appeared 4 days post-transfer. In conclusion, functional regulation of HR cells is probably achieved by enhancing cell differentiation via zGCM2 activation.