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Background: Accumulation of single nucleotide polymorphisms (SNPs) in the displacement loop (D-loop) of mitochondrial DNA (mtDNA) has been identified to be associated with cancer risk and disease outcome. In this study, we investigated whether the SNPs in mitochondrial D-loop were associated with the outcome of malignant melanoma (MM) in Chinese Han population., Methods: The D-loop region of mtDNA was sequenced for 75 MM patients recorded in the Fourth Hospital of Hebei Medical University between 2003 and 2009. The 5-year survival curve were calculated with the Kaplan-Meier method and compared by the log-rank test at each SNP site, a multivariate survival analysis was also performed with the Cox proportional hazards method., Results: The SNP sites of nucleotides T204C, A235G and T16519C were identified for prediction of post-operational survival by the log-rank test. In an overall multivariate analysis, the T204C and A235G alleles were identified as independent predictors of MM outcome., Conclusion: Genetic polymorphisms in the D-loop are independent prognostic markers for patients with MM. Accordingly, the analysis of genetic polymorphisms in the mitochondrial D-loop can help identify patient subgroups at high risk of a poor disease outcome.