Objective. Adiponectin is an adipokine that is mostly secreted from adipose tissues and has a significant role in the improvement of insulin resistant and type 2 diabetes mellitus (T2DM). This study is conducted to examine the association of rs17300539 and rs266729 with T2DM and serum adiponectin level in Iranian population. Method. A case-control study was conducted on 80 individuals with fasting plasma glucose (FPG) >100 (mg/dl) as diabetic-pre-diabetic group, and 80 individuals with fasting plasma glucose 70-100 (mg/dl) as control group. DNA extraction was done on samples and genotyping method was performed by PCR-RFLP. Result. The frequency of GA genotype in rs17300539 (diabetic/pre-diabetic 35.5%, control 11.3%, (OR [95%CI]=4.18[1.8-9.6]; p=0.001) and allele A (diabetic/pre-diabetic 31%, control 9%, (OR [95% CI]=4.67[2-10.7]) was significantly more in diabetic/pre-diabetic group compared to control group. The difference in the genotype frequency for rs266729 in diabetic group compared to that in control was not significant. The levels of adiponectin in diabetic cases had no difference compared to the control group in both polymorphisms. The rs266729 was not associated with any metabolic parameter except waist circumference (p=0.03), however, rs17300539 shows association only with fasting plasma glucose, triglyceride, and total cholesterol (p=0.007, 0.039, 0.0032, respectively). Conclusion. Our findings showed that there is an association between rs17300539 with the increase of T2DM but rs266729 showed no association with the risk of T2DM. Allele A of rs17300539 increased the risk of diabetes. There is no association between adiponectin level and both polymorphisms.