Prolong colonization of Helicobacter pylori in the stomach is the major cause that may lead to various gastric disorder including gastritis, gastric ulcer and gastric cancer. H. pylori are able to survive in high acidic environment by neutralizing the stomach acid. The neutralization may lead to several gastric disorders. By doing complete comparative genomic analysis of H. pylori strains, the specific region of gene that induces the infection of the stomach can be identified. Sequencing and comparing targeted genomic region with reference genome by using multiple genome alignment tools provide necessary foundation regarding the conserved regions. Visualization of genomic comparison helps in determination of the differences of genotype between the closely related strains. Genome sequences of H. pylori strains CPY1124 and SJM180, isolated from gastric ulcer and gastritis patients respectively, were chosen for this research analysis. These two strains were sequenced with reference genome of PeCan4, isolated from gastric cancer patient, by using Next-Generation Sequence (NGS) data. It is shown that CPY1124 have higher percentage of similarities to PeCan4. Therefore, higher percentage of cancer-causing gene of PeCan4 was predicted to be found in CPY1124 rather than SJM180. This concludes that gastric ulcer may lead to gastric cancer.