The inference of transmission pathways for medicinally important bacteria is important to our understanding of pathogens. Here we report analyses of transmission in Helicobacter pylori, a major carcinogen. Our study is novel in that the focal community comprises detailed family pedigrees and has a high prevalence of H. pylori. To infer transmission, we performed high-resolution analyses of nucleotide sequences for three genes and accounted for the occurrence of mutation and recombination through the use of simulation modeling. Our results demonstrate that transmission has a strong nonfamilial component potentially the result of a large proportion of infections derived from the community. These results are interesting from both a medical and an evolutionary standpoint. First, efficient control measures and beliefs about the sources of H. pylori infection should be reevaluated. Evolutionarily, our results contradict the hypothesis of strict vertical transmission, presented as an explanation for the strong correlation between human population history and H. pylori diversity. Thus the paradox of persistent phylogenetic structure, despite a permissive mode of transmission and high recombination rates, must be solved elsewhere. Here we consider the potential for recombination events to maintain genetic structure in light of horizontal transmission.