The purpose of the present study was to examine the distribution of the anion exchange protein in the sea lamprey. Southern blots showed that genomic DNA of juvenile lampreys possesses several regions that are similar to segments of the AE gene from other vertebrates. However, physiological experiments examining rapid anion fluxes across the red blood cell (rbc) membrane and molecular experiments examining mRNA transcript levels both indicated that the anion exchange protein is absent in sea lamprey rbcs. In contrast, lamprey kidney, skeletal muscle, liver and heart tissue all appeared to possess mRNA transcripts for an AE protein. Further evidence for the presence of an AE protein in kidney tissue was obtained from Western blots. In order to evaluate the impact of the apparent rbc anion exchange limitations, the bicarbonate permeability of lamprey rbcs was also evaluated using mass spectrometry. The bicarbonate permeability of the lamprey rbc membrane was an order of magnitude lower than that of trout rbcs. Taken together, these results indicate that the gene for the AE protein is indeed present in lampreys, but it is not expressed in the rbc. Moreover, the process of CO2 transport in lamprey probably does not involve bicarbonate transport across the rbc membrane.