Small GTPase Rho and septin family proteins are thought to be related to tumorigenesis. We have identified a Rho-guanine nucleotide exchange factor (GEF) as a binding partner for a mammalian septin Sept9b using yeast two-hybrid screening. We termed this molecule septin-associated RhoGEF (SA-RhoGEF). Molecular dissection analyses indicated that the C-terminal area of SA-RhoGEF exhibited binding to the N-terminal variable region of Sept9b. SA-RhoGEF was found by immunoprecipitation analysis to associate with septin complexes in REF52 fibroblast cells, maybe through direct interaction with Sept9b. Immunofluorescence analyses revealed the colocalization of SA-RhoGEF and Sept9b along with actin stress fibers in REF52 cells, and their colocalization along stress fibers was most likely to depend on their mutual interaction. In transient expression analyses, Sept9b inhibited SA-RhoGEF-dependent Rho activation in COS7 and HeLa cells. SA-RhoGEF and its fragments expressed in REF52 cells altered endogenous septin filament structures. To our knowledge, SA-RhoGEF is the first molecule providing a link between septins and Rho signaling.