Esophageal squamous cell carcinoma (ESCC) is the most common histologic subtype of esophageal cancerand is characterized by a poor prognosis. Determining gene changes in ESCCs should improve understandingof putative risk factors and provide potential targets for therapy. We sequenced about 55 million pair-endreads from a pair of adjacent normal and ESCC samples to identify the gene expression level and gene fusion.Sanger sequencing was used to verify the result. About 17 thousand genes were expressed in the tissues, of whichapproximately 2400 demonstrated significant differences between tumor and adjacent non tumor tissue. GO andKEGG pathway analysis revealed that many of these genes were associated with cellular adherence and movement,simulation responses and immune responses. Notably we identified and validated one fusion gene, HLA-E andHLA-B, located 1 MB apart. We also identified thousands of remarkably expressed transcripts. In conclusion,a novel fusion gene HLA-E and HLA-B was identified in ESCC via whole transcriptome sequencing, whichwould be a biomarker for ESCC diagnosis and target for therapy, shedding new light for better understandingof ESCC tumorigenesis.