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<p>Abstract</p> <p>Background</p> <p>The human gastric pathogen <it>Helicobacter pylori </it>is co-evolved with its host and therefore, origins and expansion of multiple populations and sub populations of <it>H. pylori </it>mirror ancient human migrations. Ancestral origins of <it>H. pylori </it>in the vast Indian subcontinent are debatable. It is not clear how different waves of human migrations in South Asia shaped the population structure of <it>H. pylori</it>. We tried to address these issues through mapping genetic origins of present day <it>H. pylori </it>in India and their genomic comparison with hundreds of isolates from different geographic regions.</p> <p>Results</p> <p>We attempted to dissect genetic identity of strains by multilocus sequence typing (MLST) of the 7 housekeeping genes (<it>atp</it>A, <it>efp</it>, <it>ure</it>I, <it>ppa</it>, <it>mut</it>Y, <it>trp</it>C, <it>yph</it>C) and phylogeographic analysis of haplotypes using MEGA and NETWORK software while incorporating DNA sequences and genotyping data of whole <it>cag </it>pathogenicity-islands (<it>cag</it>PAI). The distribution of <it>cag</it>PAI genes within these strains was analyzed by using PCR and the geographic type of <it>cag</it>A phosphorylation motif EPIYA was determined by gene sequencing. All the isolates analyzed revealed European ancestry and belonged to <it>H. pylori </it>sub-population, hpEurope. The <it>cag</it>PAI harbored by Indian strains revealed European features upon PCR based analysis and whole PAI sequencing.</p> <p>Conclusion</p> <p>These observations suggest that <it>H. pylori </it>strains in India share ancestral origins with their European counterparts. Further, non-existence of other sub-populations such as hpAfrica and hpEastAsia, at least in our collection of isolates, suggest that the hpEurope strains enjoyed a special fitness advantage in Indian stomachs to out-compete any endogenous strains. These results also might support hypotheses related to gene flow in India through Indo-Aryans and arrival of Neolithic practices and languages from the Fertile Crescent.</p>