Somatic mitochondrial DNA (mtDNA) alternations such as point mutations and microsatellite instability (MSI) have been found to be associated with human cancers.We reported here clinical and molecular characterization of a Chinese patient who had a family history of esophageal cancer.Clinically,we analysis the carcinoembryonic antigen (CEA) and squamous cell carcinoma (SCC) level from peripheral blood.By molecular level,we sequenced the mitochondrial Dloop region and found the co-occurrence of homoplasmic 16189T>C and heteroplasmic 310T>C variants which located in HVR1 and HVR2,respectively,resulting mtMSI might be associated with esophageal cancer.Co-existence of two sites of mtMSI in D-loop is infrequent, suggested that defects in mitochondrial transcription may be a potential mechanism for cancer development, shad additional light on the cancer diagnosis and therapy.Taken together, our data indicated that mtMSI may be served as a biomarker in the clinical and molecular diagnosis of esophageal cancer.