We have identified cDNAs encoding a second zebrafish ortholog of the human Na,K-ATPase 2 subunit. The 2b cDNA encodes a 292 amino acid-long polypeptide with 74% identity to the previously characterized zebrafish 2a subunit. By using a zebrafish meiotic mapping panel, we determined that the 2b gene (atp1b2b) was tightly linked to markers on linkage group 5, whereas the 2a gene was located on linkage group 23. In situ hybridization analysis shows that in developing zebrafish embryos, atp1b2a and atp1b2b are predominantly expressed in the nervous system. 2a transcripts were abundantly expressed throughout brain as well as spinal cord neurons and lateral line ganglia. In contrast, 2b mRNA expression was primarily detected in sensory organs, including retina, otic vesicles, and lateral line neuromast cells. These results suggest that the 2a and 2b genes play distinct roles in developing brain and sensory organs, and raise the possibility that the functions encoded by the single mammalian 2 gene may be partitioned between the two zebrafish 2 orthologs.