Citrate efflux transporters play an important role in iron longdistance transport from root to shoot. A citrate efflux transporter gene FeFRD3 (GenBank ID: MG462907) from Fagopyrum esculentum was cloned by using homology cloning strategy. FeFRD3 gene had an open reading frame (ORF) of 1 554 bp which encoded 517 amino acid residues with a predicated molecular weight of about 55.83 kD and an isoelectric point of 8.48. Bioinformatics analysis showed that FeFRD3 protein had eight transmembrane domains and located in plasma membrane or tonoplast. Protein sequence analysis indicated that FeFRD3 had a high degree of identity with FRD3 homology proteins from Arabidopsis, soybean and rice. Phylogenetic tree analysis showed that FeFRD3 belongs to the class of citrate efflux transporter with function in iron longdistance transport from root to shoot, and was most closely related to AtFRD3 of Arabidopsis. qRTPCR analysis indicated that FeFRD3 gene was expressed in root, stem, leaf and seed. Moreover, the expression level in root and seed was highest and minimal, respectively. Deficiency of iron had no effect on the expression level of FeFRD3 in root. In contrast, higher iron treatment had obviously induced for the expression of FeFRD3 in root. Research result laid a foundation for further study the function of FeFRD3 in iron longdistance transport from root to shoot in F. esculentum.