Overexpression of the genes induced by nitric oxide (NO) in EC109 esophageal carcinoma cell line was studied by using suppression subtractive hybridization (SSH), reverse mRNA dot blot and Northern blot. The nucleotide of their expressed sequence tag (EST) was sequenced and analyzed by NCBI database. The six mitochondrial DNA coding genes, ND-4L, ND-4, COX-2, Lys-tRNA, ATP-8 and ATP-6 were identified from 69 SSH positive clones. The results indicated that NO can distinctly induce overexpression of mitochondria DNA encoded genes in the esophageal carcinoma cells. In addition, it was discovered that there were single nucleotide substitution in three sites of the fragment of ND-4L and ND-4 genes (10 736～11 449, 10 872 T→C, 11 001 A→G, 11 346 A→G), and one single nucleotide deletion (8 380，A) which will lead to occur the frame-shift mutation in the peptide in the fragment of COX-2/Lys-tRNA /ATP-8/ATP-6 genes (8 011～8 589). The analysis of amino acid sequences showed that an incorrect structural ATP-8 subunit existed possibly in the EC109 cell induced by NO. These results provided a new clue for further exploring the mechanism of NO effecting on carcinoma cells.