Aluminum (Al) tolerance in wheat (Triticum aestivum L.) is mainly achieved by malate efflux, which is regulated by the expression of the recently identified gene, presumably encoding an Al-activated malate efflux transporter (ALMT1). However, the transport mechanism is not fully understood, partly as a result of the rapid turnover of its substrate. We developed a tool to study malate transport in wheat by screening biological compounds using the well-characterized Schizosaccharomyces pombe malate transporter (SpMAE1). Expression of SpMAE1 in both S. pombe and Saccharomyces cerevisiae, which has no SpMAE1 homologue, caused hypersensitivity to thio-malic acid. This hypersensitivity was prominent at pH 3.5, but not pH 4.5, and was accompanied by an increase in thiol content, indicating that SpMAE1 mediates the uptake of thio-malic acid at a specific low pH. In wheat, root apices were able to accumulate thio-malic acid without growth reduction at pH values above 4.2. Pretreatment of root apices with thio-malic acid followed by Al treatment induced thio-malate efflux. Al-induced thio-malate efflux was much higher in Al-resistant cultivars/genotypes than in Al-sensitive ones, and was accompanied by a decrease in thiol-content. Thio-malate efflux in the Al-resistant cultivar was slightly activated by lanthanum or ytterbium ion. Thio-malic acid did not alleviate the Al-induced inhibition of root elongation in wheat. Taken together, our results suggest that thio-malate acts as an analogue for malate in malate transport systems in wheat and yeast, and that it may be a useful tool for the analysis of malate transport involved in Al-tolerance and of other organic ion transport processes.