Abstract: The bacterial flagellum represents one of the best understood molecular machines. Comprised of 40 parts that self-assemble into a true rotary engine, the biochemistry and genetics of these systems has revealed an unanticipated complexity. An essential component to assembly is the subset of parts that function as a protein secretory pump to ensure and discriminate that the correct number of protein subunits and their order of secretion is precisely regulated during assembly. Of further interest is the recognition of late that a number of important plant and animal pathogens use a related protein secretory pump fused to a membrane-spanning needle-like syringe by which a subset of toxins can be injected into target host cells. Together, the flagellar and virulence protein pumps are referred to as Type III Secretion Systems (TTSS). The archetype for TTSS systems has been the pathogenic members of the genus Yersinia which includes the organism responsible for bubonic plague, Y. pestis. Our interest in the Yersinia centers on the coordinate genetic regulation between flagellum biosynthesis and virulence TTSS expression. Y. enterocolitica, for example operates three TTSSs (motility, Ysa, and Yop), but each is expressed under defined mutually exclusive conditions. Y. pestis has lost the ability to assemble flagella (the genes are present on the chromosome) and expresses only the Yop system at 37oC, mammalian temperature. Using a combination of microarray analysis, genetic fusions, and behaviors of specific engineered mutants, we demonstrate how environmental factors influence gene expression of these multigene families, where the influence is exerted within each system, and propose why segregating these systems is critical for the organism. Our model further offers an explanation as to why an important subset of human pathogens has lost motility during their histories.