Helicobacter pyloriis involved in the etiology and severity of several gastroduodenal diseases; however, plasticity of theH. pylorigenome makes complete genome assembly difficult. We report here the full genomes ofH. pyloristrains CHC155 and VN1291 isolated from a non-cardia gastric cancer patient and a duodenal ulcer patient, respectively, and their virulence demonstrated by in vitro infection. Whole-genome sequences were obtained by combining long- and short-reads with a hybrid-assembly approach. Both CHC155 and VN1291 genome possessed four kinds of genomic island: acagpathogenicity island (cagPAI), two type 4 secretion system islands within an integrative and conjugative element (tfsICE), and prophage. CHC155 and VN1291 carried East Asian-typecagAandvacAs1m1, and outer membrane protein genes, including two copies ofoipA. Corresponded to genetic determinants of antibiotic resistance, chromosomal mutations were identified in CHC155 (rdxA, gyrA, and23S rRNA) and VN1291 (rdxA,23S rRNA, andpbp1A). In vitro infection of AGS cells by both strains induced the cell scattering phenotype, tyrosine phosphorylation of CagA, and promoted high levels of IL8 secretion, indicating fully intact phenotypes of thecagPAI. Virulence genes in CHC155 and VN1291 genomes are crucial forH. pyloripathogenesis and are risk factors in the development of gastric cancer and duodenal ulcer. Our in vitro studies indicate that the strains CHC155 and VN1291 carry the pathogenic potential.