Buckwheat is an old crop whose seeds are under-utilized. The protein composition of these seeds, however, makes them suitable as much needed ingredients for the production of gluten-free products. Several buckwheat species and local cultivars are known worldwide. In this work, 1D and 2D electrophoresis were used to characterize and compare the seed protein profiles of two buckwheat species (Fagopyrum esculentum and Fagopyrum tataricum). The two analyzed cultivars of F. esculentum represent authentic landraces of an Italian Alpine valley, named Valtellina. The protein profiles of F. tataricum and the two F. esculentum cultivars did not show major differences. However, narrow but significant differences were present between these two landraces, allowing their discrimination at protein level. This work represents a molecular-based approach to the designation of origin and authenticity of local buckwheat varieties and their tracing in flours for human food