Objective Type 2 diabetes mellitus (T2DM) as a common disease around the world becomes a great threat to the health of human beings. The cynomolgus T2DM model, which preferably simulates human T2DM onset and progress, can be beneficial to the drug development and clinical treatment. In the present study, 37 of T2DM-susceptibility SNPs and the extended genome sequences were used to obtain corresponding SNPs in the T2DM cynomolgus monkeys. Methods Firstly, DNA pool screening was conducted. Then, using polymerase chain reaction to amplify and to sequence the cynomolgus homologous sequences. Using DNAStar software to analyze the differences between bases. Finally, we used analysis of variance and F test to calculate the frequency of alleles. We also used the GLM models of SAS software to analyze the association of genotype with fasting plasma glucose and glycosylated hemoglobin. Results SNP661A, SNP661B, SNP343A, SNP343B, SNP343C, SNP565A, SNP565B and SNP565C were found to have a significant difference of allele frequencies between spontaneous cases and controls. Conclusions The findings of this study suggest that SNP661A, SNP661B, SNP343A, SNP343B and SNP343C may play an important role in the establishment of cynomolgus T2DM models.