show Abstracthide AbstractThe stomach bacterium Helicobacter pylori is one of the most prevalent human pathogens. It has dispersed globally with its host for the past 100,000 years leading in a distinct phylogeographic pattern in modern H. pylori populations. This phylogeography is used to deduce both recent and ancient human migrations (1, 2). Owing to the complex demographic history of Europe, different hypotheses about the origin of the extant European H. pylori population (hpEurope) exist (3, 4). Here, we present a 5,300-year-old high-coverage H. pylori genome from a European Copper Age glacier mummy. Comparative sequence analysis with contemporary H. pylori classifies the “Iceman” Helicobacter as a cagA positive vacA s1a/i1/m1 type strain, most closely resembling a strain that today is commonly found in Central and South Asia and that substantially shaped the genomes of modern European H. pylori strains.