Smooth septate junctions (sSJs) are cell-cell junctions that are thought to regulate the paracellular pathway of the intestine and renal system in arthropods. The detailed mechanism of action of sSJs is not well understood, because their molecular organization has remained elusive for a long time. Recently, two sSJ-specific membrane proteins, Ssk and Mesh, were identified by screening monoclonal antibodies raised against sSJ-containing membrane fractions isolated from the silkworm midgut. Furthermore, a genetic screen in Drosophila based on microscopic observation of sSJ formation identified Tsp2A as a novel sSJ-specific membrane protein. Together with Tsp2A, Ssk and Mesh form a protein complex, and all three proteins are required for sSJ formation, as well as intestinal barrier function in Drosophila. Additional studies are likely to elucidate their roles in (1) the formation and reorganization of sSJs, (2) paracellular barrier functions and permselectivity, and (3) short-term and long-term regulation of paracellular functions in arthropod epithelia.