Multidrug and toxic compound extrusion (MATE) proteins are widely present in bacteria, fungi, plants and mammals. Recent studies have showed that a group of plant MATE genes encodes citrate transporter, which are involved in the detoxification of aluminium or translocation of iron from the roots to the shoots. In this study, we isolated two homologous genes (ScFRDL1 and ScFRDL2) from this family in rye (Secale cereale L.). ScFRDL1 shared 94.2% identity with HvAACT1, an Al-activated citrate transporter in barley (Hordeum vulgare L.) and ScFRDL2 shared 80.6% identity with OsFRDL2, a putative Al-responsive protein in rice (Oryza sativa L.). Both genes were mainly expressed in the roots, however, they showed different expression patterns. Expression of ScFRDL1 was unaffected by Al treatment, but up-regulated by Fe-deficiency treatment. In contrast, expression of ScFRDL2 was greatly induced by Al but not by Fe deficiency. The Al-induced up-regulation of ScFRDL2 was found in both the root tips and basal roots. Furthermore, the expression pattern of ScFRDL2 was consistent with citrate secretion pattern. Immunostaining showed that ScFRDL1 was localised at all cells in the root tips and central cylinder and endodermis in the basal root. Taken together, our results suggest that ScFRDL1 was involved in efflux of citrate into the xylem for Fe translocation from the roots to the shoots, while ScFRDL2 was involved in Al-activated citrate secretion in rye.