The hook length of the flagellum is controlled to about 55 nm in Salmonella. The flagellar type III protein export apparatus secretes FliK to determine hook length during hook assembly and changes its substrate specificity from the hook protein to the filament protein when the hook length has reached about 55 nm. Salmonella FliK consists of an N-terminal domain (FliK n , residues 1-207), a C-terminal domain (FliK c , residues 268-405) and a flexible linker (FliK L , residues 208-267) connecting these two domains. FliK n is a ruler to measure hook length. FliK c binds to a transmembrane export gate protein FlhB to undergo the export switching. FliK L not only acts as part of the ruler but also contributes to this switching event, but it remains unknown how. Here we report that FliK L is required for efficient interaction of FliK c with FlhB. Deletions in FliK L not only shortened hook length according to the size of deletions but also caused a loose length control. Deletion of residues 206-265 significantly reduced the binding affinity of FliK c for FlhB, thereby producing much longer hooks. We propose that an appropriate length of FliK L is required for efficient interaction of FliK c with FlhB.