Background: Genetic factors contribute to essential hypertension (EH) etiology, however, causal genes haven’t been identified. Mitochondrial dysfunction is common in EH. However, evidence supporting mitochondrial DNA (mtDNA) mutation involved in EH in Chinese Han is lacking. We aimed to characterize relationship between mtDNA mutation and EH in China.Methods: Totally 216 individuals including 151 EH patients and 65 controls from Chinese Han population in Xinjiang were sequenced for whole mtDNA genome. Novel variations and haplogroups were identified for each mtDNA sequence. Frequencies of gene mutations were compared between cases and controls, and functional changes of mtDNA genes associated with EH were predicted.Results: Haplogroups of Chinese Han population in Xinjiang were consistent with those in northern China. No association of mitochondrial haplogroup with EH was observed. Nine novel variations and three EH-associated mutations were identified. Variants in mutation m.12361A>G, m15662A>G and m.1598G>A were predicted to affect functions of ND5, CYTB and 12S rRNA, respectively.Conclusions: Our results have provided a new clue for mitochondrial genetic characteristics in etiology of EH in Chinese Han population in Xinjiang.