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<i>Helicobacter pylori</i> uses a cluster of polar, sheathed flagella for swimming motility. A search for homologs of <i>H. pylori</i> proteins that were conserved in <i>Helicobacter</i> species that possess flagellar sheaths but were underrepresented in <i>Helicobacter</i> species with unsheathed flagella identified several candidate proteins. Four of the identified proteins are predicted to form part of a tripartite efflux system that includes two transmembrane domains of an ABC transporter (HP1487 and HP1486), a periplasmic membrane fusion protein (HP1488), and a TolC-like outer membrane efflux protein (HP1489). Deleting <i>hp1486</i>/<i>hp1487</i> and <i>hp1489</i> homologs in <i>H. pylori</i> B128 resulted in reductions in motility and the number of flagella per cell. Cryo-electron tomography studies of intact motors of the Δ<i>hp1489</i> and Δ<i>hp1486</i>/<i>hp1487</i> mutants revealed many of the cells contained a potential flagellum disassembly product consisting of decorated L and P rings, which has been reported in other bacteria. Aberrant motors lacking specific components, including a cage-like structure that surrounds the motor, were also observed in the Δ<i>hp1489</i> mutant. These findings suggest a role for the <i>H. pylori</i> HP1486-HP1489 tripartite efflux system in flagellum stability. Three independent variants of the Δ<i>hp1486</i>/<i>hp1487</i> mutant with enhanced motility were isolated. All three motile variants had the same frameshift mutation in <i>fliL</i>, suggesting a role for FliL in flagellum disassembly.