Bicarbonate (HCO3-) transporters play crucial roles in cell-signaling pathways and are essential for cell viability. Here we describe the first cloning and localization of a HCO3- transporter from sperm of the sea urchin, Strongylocentrotus purpuratus. The deduced protein is 1214 amino acids and has a calculated molecular mass of 135 kDa. The annotated protein coding region of the transporter gene consists of 24 exons. The most similar human protein is the Na+/HCO3- cotransporter-2 (NBC2), which has 53% identity and 68% similarity to the sea urchin protein. The sea urchin protein shares the major structural features of HCO3- transporters, including 13 transmembrane segments, a DIDS (4,4-diiodothiocyanatostilbene-2, 2-disulfonic acid) binding motif and N-linked glycosylation sites. It has longer N- and C-terminal cytoplasmic domains compared to human HCO3- transporters. The sea urchin protein possesses a relatively long 3rd extracellular loop with four conserved cysteine residues. This is characteristic for Na+/HCO3- cotransporters, but not for anion exchangers, suggesting that the sea urchin protein is a Na+/HCO3- cotransporter. It is therefore designated as Sp-NBC. A neighbor-joining tree shows that Sp-NBC branches closer to the electroneutral type of HCO3- transporters. Western immunoblots and immunoflourescence show that Sp-NBC is concentrated in the flagellar plasma membrane, suggesting a role in motility regulation.