The apical junctional complex (AJC), encompassing the tight junction (TJ) and adherens junction (AJ) plays a vital role in regulating epithelial cell differentiation and barrier function of simple epithelia. Both AJ and TJ are comprised of multiprotein complexes consisting of transmembrane proteins, which interact with the underlying cytoskeleton via cytoplasmic scaffold proteins. These interactions are tightly controlled by a number of signaling proteins that are critical for the regulation of the AJC function. Among these signaling molecules Rho family of small GTPases have been demonstrated to regulate the AJC function in diverse physiological and pathological states. In this review we will focus on experimental data addressing the role of Rho GTPase family members, Rho, Rac and Cdc42 in the regulation of epithelial AJC, and analyze Rho GTPase-mediated signaling pathways that control maintenance, disassembly and assembly of the AJC in epithelial cells.