Mitochondrial single nucleotide polymorphisms (SNPs) are significantly correlated with the development of diabetes mellitus. However, these polymorphisms are emerging to be considerably diverse among different population and regions. Sivaganga district is recently being given importance for genetic studies due to its rigid family structure. Hence, the present study is planned to investigate the correlation between mitochondrial SNP of ND1 gene with type II diabetes (T2D) of Karaikudi population of Sivaganga district. For this study, 206 samples including 105 T2D and 101 healthy volunteers were collected and screened for ND1 gene mutation. Genotyping for the ND1 gene was characterized by polymerase chain reaction, Restriction fragment length polymorphism (RFLP) followed by sequencing. In addition, clinical and biochemical variables were analyzed. RFLP and sequencing results showed G[A transition at 3316 position of ND1 gene in both T2D (6.67 %) and in control subjects (1.9 %). Since the frequency of the mutation was found high in T2D patients, we screened for the mutation in their family members and identified its maternal mode of inheritance. The result warrants for the detailed study to identify population based mitochondrial mutation association with disease development.