Rhodobacter sphaeroides has two different sets of flagellar genes. Under the growth conditions commonly used in the laboratory, the expression of the fla1 set is constitutive, whereas the fla2 genes are not expressed. Phylogenetic analyses have previously shown that the fla1 genes were acquired by horizontal transfer from a gammaproteobacterium and that the fla2 genes are endogenous genes of this alphaproteobacterium. In this work, we characterized a set of mutants that were selected for swimming using the Fla2 flagella in the absence of the Fla1 flagellum (Fla2 ؉ strains). We determined that these strains have a single missense mutation in the histidine kinase domain of CckA. The expression of these mutant alleles in a Fla1؊ strain allowed fla2-dependent motility without selection. Motility of the Fla2 ؉ strains is also dependent on ChpT and CtrA. The mutant versions of CckA showed an increased autophosphorylation activity in vitro. Interestingly, we found that cckA is transcriptionally repressed by the presence of organic acids, suggesting that the availability of carbon sources could be a part of the signal that turns on this flagellar set. Evidence is presented showing that reactivation of fla1 gene expression in the Fla2؉ background strongly reduces the number of cells with Fla2 flagella. More than 40 genes are involved in the biogenesis and functioning of the bacterial flagellum. This structure has three major subcomponents, the basal body, the hook, and the filament. The basal body contains the export apparatus, an inner membrane ring (MS ring), a periplasmic ring (P ring), and, depending on the species, an outer membrane ring (L ring). The basal body also includes the flagellar motor and a rod that expands from the MS ring and crosses the L and P rings. The hook is the first extracellular structure that is assembled; it connects the basal body with the flagellar filament that is formed by thousands of flagellin subunits (reviewed in references 1-3).In most bacterial species, the expression of the flagellar genes is highly regulated and frequently follows a hierarchical order in which the late genes are expressed until the early genes, that are higher in the hierarchy, are expressed. At the top of the hierarchy, a transcriptional regulator is responsible for the expression of the genes required to assemble the early flagellar structures that are located in the cytoplasm (i.e., export apparatus), in the cytoplasmic membrane (i.e., MS ring), and, depending on the hierarchy, in the periplasm (i.e., P ring), the outer membrane (i.e., L ring), and the extracellular milieu (i.e., hook). Within this class, additional transcription factors are expressed. These proteins are required to transcribe the late genes, such as fliC (flagellin), fliD (filament cap), and fliS