The CrCAX1 gene encoding a Ca 2+/H + and Na +/H + exchanger was cloned and characterized from the unicellular green alga Chlamydomonas reinhardtii to begin to understand the mechanisms of cation homeostasis in this model organism. CrCAX1 was more closely related to fungal cation exchanger (CAX) genes than those from higher plants but has structural characteristics similar to plant Ca 2+/H + exchangers including a long N-terminal tail. When CrCAX1-GFP was expressed in Saccharomyces cerevisiae, it localized at the vacuole. CrCAX1 could suppress the Ca 2+-hypersensitive phenotype of a yeast mutant and mediated proton gradient-dependent Ca 2+/H + exchange activity in vacuolar membrane vesicles. Ca 2+ transport activity was increased following N-terminal truncation ofCrCAX1, suggesting the existence of an N-terminal auto-regulatory mechanism. CrCAX1 could also provide tolerance to Na + stress when expressed in yeast or Arabidopsis thaliana because of Na + /H + exchange activity. This Na + /H + exchange activity was not regulated by the N terminus of the CrCAX1 protein. A subtle tolerance by CrCAX1 in yeast to Co 2+ stress was also observed. CrCAX1 was transcriptionally regulated in Chlamydomonas cells grown in elevated Ca 2+ or Na +. This study has thus uncovered a novel eukaryotic proton-coupled transporter, CrCAX1, that can transport both monovalent and divalent cations and that appears to play a role in cellular cation homeostasis by the transport of Ca 2+ and Na + into the vacuole. © 2009 by The American Society for Biochemistry and Molecular Biology, Inc.