The exquisite sensitivity of the cochlea, which mediates the transduction of sound waves into nerve impulses, depends on the endolymph ionic composition and the endocochlear potential. A key protein in the maintenance of the electrochemical composition of the endolymph is the Na,K-ATPase. In this study, we have looked for the presence in the rat inner ear of members of the FXYD protein family, recently identified as tissue-specific modulators of Na,K-ATPase. Only FXYD6 is detected at the protein level. FXYD6 is expressed in various epithelial cells bordering the endolymph space and in the auditory neurons. FXYD6 co-localizes with Na,K-ATPase in the stria vascularis and can be co-immunoprecipitated with Na,K-ATPase. After expression in Xenopus oocytes, FXYD6 associates with Na,K-ATPase ␣1-1 and ␣1-2 isozymes, which are preferentially expressed in different regions of the inner ear and also with gastric and non-gastric H,K-ATPases. The apparent K ؉ and Na ؉ affinities of ␣1-1 and ␣1-2 isozymes are different. Association of FXYD6 with Na,K-ATPase ␣1-1 isozymes slightly decreases their apparent K ؉ affinity and significantly decreases their apparent Na ؉ affinity. On the other hand, association with ␣1-2 isozymes increases their apparent K ؉ and Na ؉ affinity. The effects of FXYD6 on the apparent Na ؉ affinity of Na,KATPase and the voltage dependence of its K ؉ effect are distinct from other FXYD proteins. In conclusion, this study defines the last FXYD protein of unknown function as a modulator of Na,K-ATPase. Among FXYD protein, FXYD6 is unique in its expression in the inner ear, suggesting a role in endolymph composition.