Taking nanyang grey wheat and hard purple wheat, common purple wheat, blue wheat as the samples, zhoumai16 and yanzhan 4 110 as control group, the distribution and content of trace element selenium in wheat was digested by microwave; the trace element selenium in wheat skin, kernel and whole wheat flour were determined by molecular fluorescence. The results showed that the detection limit of selenium was 3.6×10-2 ng/mL, recovery was 96.88~104.23%. Selenium content was 0.064 3~0.136 mg/kg in all wheat flour, 0.100~0.155 mg/kg in wheat skin and 0.055 3~0.116 mg/kg in wheat kernel. Selenium content in the color wheat skin was more than that in two kinds of common wheat;selenium content was the highest in common purple wheat, which can be used as good dietary source of selenium for people.