Buckwheat sprouts are a vegetable which provides health benefit with their nutritionally important substances. Buckwheat has been considered as preventive medicine in the last decade. The present study was focused on the reference maps common (Fagopyrum esculentum Möench.) and tatary(Fagopyrum tataricum Gaertn.) buckwheat leaf and stem cultured in light and dark condition. Proteins were extracted from 7-day germinated buckwheat sprout sand separated by two-dimensional electrophoresis(2-DE) with isoelectro focusing gel over pH3 to 10. A total of more than 1520 protein spots were revealed on 2-DE gel, in which 165 proteins were identified in the basis of peptide mass fingerprinting. Functional category analysis indicated that these differentially expressed proteins mainly involved in cellular process, defense responsive, energy production, metabolism, photosynthesis, DNA recombination, DNA replication, seed storage, signal transduction, stress responsive, transcription, translation, and energy transport proteins. The pattern at protein level suggested the important roles for energy and protein metabolism-related proteins in growing sprouts under dark and light condition, accompanied by the activated of the stress responsive and growth condition. The proteomic profiling of common and tatary buckwheat will give insight for understanding buckwheat physiology and application to buckwheat industry.