Objective To investigate the relationship between mitochondrial fusion gene polymorphism and essential hypertension in Hakka population in southern China. Methods 100 patients with primary hypertension from Hakka people in southern China were selected as the observation group of this study, and 46 non-hypertensive patients in the same period were selected as the control group of this study. The general data of the two groups were collected, and the polymorphism of mitochondrial fusion gene, allele frequency and Hardy Weinberg balance were analyzed. The association between mitochondrial fusion gene polymorphism and essential hypertension in Hakka population in southern China was analyzed by Odds ratios (OR) and 95% Confidence interval (CI). Results There was no significant difference in age, TG, HDL, FPG, UA, Cr and UN between the observation group and the control group (P＞0.05). There were significant differences in SBP, DBP, TC and LDL (P＜0.05). The expression of AG in rs11916762 and rs 7620017, TT in rs 2336384, GG in rs 2236057, GT in rs 7620342 and AA+AG in rs 11925699 in the observation group was higher than that in the control group (P＜0.05). The gene distribution of each site was consistent with Hardy-Weinberg equilibrium law (P＞0.05). The AA and AG genotypes at rs 11916762, rs 2236057 and rs 11925699, the AA and GG genotypes at rs 7620017, the GG genotypes at rs 2336384, and the GG, GT and TT at rs 7620342 of mitochondrial fusion genes were associated with the southern Chinese gene. There was correlation between essential hypertension in family (P＜0.05).Conclusion There is a positive correlation between mitochondrial fusion genes (Mfn1,Mfn2, Opa1) and essential hypertension in the Hakka population in southern China. Mitochondrial fusion genes as molecular markers have application value in the monitoring of essential hypertension in the Hakka population in southern China