<p><i>Helicobacter pylori</i> is commonly found in the upper gastrointestinal tract of over 50% of the global population. There is growing recognition of the importance of <i>Helicobacter pylori</i> infections, specifically gastric cancer, and a clear gap in the literature about the clinical and epidemiological studies on the pathogen, especially in Iraq. Therefore, this study aimed to analyze the genetic diversity and phylogeographic origins of <i>Helicobacter pylori</i> strains in Iraq and their relationship to global phylogeographic groups using MLST. This cross-sectional study involved 203 biopsy specimens from patients admitted to the gastroenterology units, biopsy specimens were cultured on selective media and identified as <i>Helicobacter pylori</i>. DNA was extracted, and PCR was used for molecular identification, and phylogeographic analysis was performed, for which primers were taken from the MLST website. The sequences were aligned and submitted to the MLST database. Molecular polymorphism analysis revealed the identification of 112 new alleles. Phylogenetic analysis using the TBTool software was investigated for these <i>Helicobacter pylori</i> isolates, which showed that the 19 unique STs can be classified into five clusters. Data from this study showed that <i>Helicobacter pylori</i> strains were in the same cluster as isolates from the Middle East area. Results revealed that the clinical isolates identified from this study were like their European ancestors and belonged to the hpEurope haplotype. The study concluded that the population structure of <i>Helicobacter pylori</i> strains in Iraq was closely similar to their European counterparts and belonged to the hpEurope haplotype. No isolates were identified from the hpAfrica or hpEastAsia sub-populations.</p>