Tartary buckwheat (Fagopyrum tataricum, TB) is an important functional food containing proteins with balanced amino acid composition and more flavonoids than common buckwheat (Fagopyrum esculentum, CB). Buckwheat contains highly potent allergens that trigger an allergic reaction via an IgE mediated response. In this work, the full-length cDNA encoding Fag t 2 from tartary buckwheat seeds was cloned by screening the cDNA library of seed-filling period. The recombinant Fag t 2 (rFag t 2) expressed in Pichia pastoris SMD1168H was purified by purified by immobilized metal affinity chromatography. It demonstrated that Fag t 2 was a major allergen in tartary buckwheat with the activity of IgE binding and pepsin resistance, along with the thermal stability. The identification of natural Fag t 2 (n Fag t 2) confirmed that the Fag t 2 protein belongs to the 2S albumin family, only existing in embryo. Most interesting, we discovered that Fag t 2 had a α-amylase inhibitor domain near the end of C-terminal. The possible activity of α-amylase inhibitor of Fag t 2 will be detected in subsequent studies.