The flagellar motor switch complex protein FliG plays an essential role in flagella biosynthesis and motility. In most motile bacteria, only one fliG homologue is present in the genome. However, several spirochete species have two putative fliG genes (referred to as fliG1 and fliG2) and their roles in flagella assembly and motility remain unknown. In this report, the Lyme disease spirochete Borrelia burgdorferi was used as a genetic model to investigate the roles of these two fliG homologues. It was found that fliG2 encodes a typical motor switch complex protein that is required for the flagellation and motility of B. burgdorferi. In contrast, the function of fliG1 is quite unique. Disruption of fliG1 did not affect flagellation and the mutant was still motile but failed to translate in highly viscous media. GFP-fusion and motion tracking analyses revealed that FliG1 asymmetrically locates at one end of cells and the loss of fliG1 somehow impacted one bundle of flagella rotation. In addition, animal studies demonstrated that the fliG1- mutant was quickly cleared after inoculation into the murine host, which highlights the importance of the ability to swim in highly viscous media in the infectivity of B. burgdorferi and probably other pathogenic spirochetes.