Background: The response to neoadjuvant chemoradiotherapy (nCRT) for locally advanced esophageal squamous cell carcinoma (ESCC) can vary, but there is still no biomarker that can identify the benefiting population. Therefore, biomarkers to predict the outcome of nCRT are needed, as well as elucidation of the mechanism of resistance therapy. We investigated differences of genomic characteristics between patients with a pathologic complete response (pCR) and those with little or no response (pathologic stable disease: pSD) before and after nCRT. Methods: Fourteen subjects with locally advanced ESCC (7 cases of pCR and 7 of pSD) who received nCRT before undergoing esophagectomy were enrolled. An analysis of whole-exome sequencing (WES) data from 27 ESCC tissue samples obtained from the subjects pre and post nCRT was performed. Results: The number of pretherapy samples displaying loss of chromosome 19p13.11 was higher in the pCR group than in the pSD group (5/6) (P=0.0291, Fisher's exact test). Gain of 19q13.31 was observed significantly more often in the samples obtained following nCRT (5/14). KMT2A missense mutation was found more frequently in the pSD group's pre-nCRT samples than in those of the pCR group (3/6), and following nCRT, new genes such as NP!, KMT2D, NOTCH2, and NIPBL were detected new variations. C/G>G/C (P=0.003) and C/G>A/T (P=0.002) transitions were statistically significantly reduced in every patient after nCRT, with similar observations made in both groups (pCR group: C/G>G/C, P=0.027; C/G>ATT, P=0.004; and pSD group: CJG>G/C, P=0.032; C/G>A/T, P=0.017). Conclusions: Biomarkers to predict pCR might include 19p13.11 copy number loss and KMT2A missense mutation. Further validation in a prospective study of a larger sample is required.