The fish pathogen Vibrio alginolyticus contains two unique flagellar systems. The LuxS quorum sensing system is reported to regulate the expression of virulence factors in a wide variety of pathogenic bacteria. Our previous work demonstrated that inactive luxS led to decreased virulence in V. alginolyticus. In this study, LuxS-dependent regulation of motility and flagella biogenesis, the potential virulence factors in V. alginolyticus, were further investigated. A luxS-deleted mutant showed deficiency in motility and flagella formation, and an intact luxS complemented the defect. Since motility is flagella dependent, V. alginolyticus flagella biogenesis related genes, including the flagella regulator genes flaK and lafK and the sub-hierarchical flagellar genes fliS and lafA, were cloned and identified. Based on quantitative real-time reverse transcription-PCR, differential expression of these genes was confirmed in wild-type and luxS mutants. Our results indicate that LuxS plays an important role in the regulation of motility and flagella biogenesis in V. alginolyticus.