【Objective】To identify the difference of mitogen-activated protein kinase gene (MAPK) sequences among intraspecific common buckwheat, Fagopyrum esculentum, and study the sequence change during the chronical domestication process. 【Method】 The common buckwheat varieties, containing nine cultivars and three wild types with shattering habit, were selected for PCR amplification of the conservative fragments of MAPK gene. Sequences were analyzed and protein conformations were predicted. 【Result】 The full length of buckwheat MAPK cDNA was 2 835 bp, the length of the open readling frame (ORF) was 1 827 bp, and 609 amino acids containing the TDY tripeptide module were encoded. The buckwheat MARK belonged to the group D of plant MARK proteins. A total of 723 invariable sites and 70 polymorphic sites in MAPK sequence of common buckwheat were identified in 12 tested materials. We did not find difference among the ORF sequences of nine cultivars, neither among three wild types. There were eight differential nucleotides in the ORF of MAPK gene which encoded three amino acid polymorphisms between the cultivars and wild types. We found a change of α-helix conformation which was induced by transforming histidine (H) to tyrosine (Y) at the 13th site in the ORF of MARK. 【Conclusion】 The MAPK sequence is highly conserved and the 13th amino acid site has been highly consistently selected during the chronical process of domestication.