Abstract: The deoxyribonucleic acid (DNA) in the human genome was extracted from the human blood by the improved Miller method. The DNA fragments including SNP loci were amplified, and the remaining dNTPs and primers were digested using CIP and Exo I. Then the base on the SNP loci was determined by the single base extension reaction. Finally, the base was identified from the molecular weight difference between the extension product and extension primer by bio mass spectrometry (MALDI TOFMS or ESI QqTOFMS). The advantages and disadvantages of the different bio mass spectrometry including MALDI TOFMS and ESI QqTOFMS used to measure SNP genotyping were discussed,and different bio mass spectrometry methods with the other current detecting methods used to detecting SNP genotyping was compared.