Verticillium　wilt　of　cotton　is　a　soil-borne　vascular　bundle　disease.　There　is　still　a　lack　of　effective　methods　for　controlling　and　preventing　Verticillium　wilt　of　cotton.　There　are　few　reports　on　the　research　of　the　mechanism　by　which　flagellin　S　(FLiS)　protein　induces　cotton　immunity.　The　mechanism　by　which　the　FLiS　protein　induces　immune　responses　in　cotton　was　analyzed　through　prokaryotic　expression　and　purification,　physiological　and　biochemical　techniques,　and　qRT-PCR　(quantitative　real-time　polymerase　chain　reaction)　technology.　The　purpose　of　this　study　was　to　determine　the　role　and　mechanism　of　FLiS　in　improving　the　resistance　of　cotton　to　Verticillium　wilt.　An　endophytic　bacterium　(Pseudomonas)　was　isolated　from　the　roots　of　upland　cotton　cultivar　Zhongmian　44,　and　the　FLiS　gene　was　cloned.　The　FLiS　protein　purified　in　vitro　can　induce　a　hypersensitive　response　(HR)　in　tobacco,　indicating　that　it　is　an　active　protein.　In　addition,　it　is　capable　of　triggering　an　immune　response　in　upland　cotton,　thereby　enhancing　the　resistance　to　Verticillium　wilt.　The　FLiS　protein　can　induce　the　production　of　hydrogen　peroxide(H2O2),　callose,　and　defense　enzymes　in　cotton,　as　well　as　the　expression　of　disease　resistance　genes　in　the　signaling　pathways　of　salicylic　acid　(SA)　and　jasmonic　acid　(JA).　FLiS　can　be　used　as　a　biological　regulator　to　improve　the　resistance　of　upland　cotton　to　V.　dahliae.