Significance Many important bacterial pathogens such as Vibrio cholerae and Helicobacter pylori use a sheathed flagellum as the main organelle for motility. Although bacterial flagella have been extensively studied in model systems such as Escherichia coli and Salmonella , relatively little is known about sheathed flagella. In this study, we use high-throughput cryoelectron tomography to visualize thousands of polar flagella in Vibrio alginolyticus . We not only reveal unprecedented details of sheathed flagella in V. alginolyticus but also uncover key differences between sheathed flagella and unsheathed flagella in the same Vibrio species. Our studies provide insight into the unique aspects of sheathed flagella, which are effectively used by many bacterial pathogens to establish infection and disseminate in humans and other mammalian hosts.