Abstract: The chalcone synthase genes of common wheat, blue-grained wheat, and quack grass were analyzed. The composition of amino acid sequences, molecular structure, physicaland chemical characters, subcellular localization, transmembrane helices, and molecular phylogenetic evolution, secondary and tertiary structure from NCBI were analyzed and predicted by bioinformatics software. The results demonstrated that the length of three CHS genes were all 1.2 kb, which coded 394 aa and had a high homology amino acid ,and they were all unstable protein, strong hydrophobic, secondary structures of the protein were most of alpha helix, but the structure had many differences, in the other prediction protein. In the evolutionary tree could be seen the blue-grained wheat and quack grass genetic relationship is close. The result implied the properties of CHS in the Triticeae crops was almost as the same as them of other plants. This study provided the basis of research the enzymes and their genes in further step.