The dual-specificity kinase DYRK3 controls formation and dissolution of several intracellular condensates thereby regulating various cell physiological processes. Here we report that DYRK3 establishes a dynamic equilibrium between condensation and dissolution of proteins associated with membranous structures of the early secretory pathway to organize membrane traffic between the ER and the Golgi complex in mammalian cells. This depends on the peripheral membrane protein Sec16A, whose N-terminal disordered region forms DYRK3-controlled liquid-like condensates on the surface of the ER and co-phase separates with multiple ER exit site components and a subset of matrix proteins specifically associated with ERGIC and cis-Golgi. Our findings support a mechanism whereby multiple interacting and differentially regulated intracellular condensates create favorable environments for directional membrane traffic in eukaryotic cells.Recently, liquid-liquid phase separation (LLPS) has emerged as a general mechanism to locally concentrate multiple factors involved in complex biochemical processes (17)(18)(19)(20).This typically involves weak multivalent interactions between proteins with intrinsically disordered regions (IDRs)(21-24). The resulting biomolecular condensates display rapid, liquid-like merging and can exchange components between the condensed and the dilute phase within seconds. Sec16A is also a highly disordered protein, with ~75% of its total sequence predicted to be disordered in both S. cerevisiae and H. sapiens, as well as other ERES proteins including the transmembrane proteins TANGO1L (transport and Golgi organization protein 1) and cTAGE5 (cutaneous T cell lymphoma-associated antigen 5) (25,26). Moreover, ERES components can exchange with a cytosolic pool within seconds, and individual ERES can rapidly merge with each other(27-29). Thus, the mechanism by which Sec16A acts as a central organizer of ERES may involve LLPS, which drives the formation of ER-associated biomolecular condensates that locally concentrate ERES proteins and COPII vesicle coat components. This behavior may also underlie the formation of Sec bodies in drosophila S2 cells, which are membraneless organelles formed by Sec16A during amino acid starvation(30). In addition, some COPII coat components partition into stress granules(31), which are membraneless organelles formed by LLPS during stress(32, 33), suggesting an affinity for biomolecular condensates.As recently suggested(34), LLPS may also underly the formation of the Golgi matrix (35). This matrix consists of golgins, which are transmembrane or membrane-associated proteins with long coiled-coil regions in their cytosolic domains (36,37). The cis-golgin GM130 has recently been shown to undergo LLPS in vitro and when overexpressed in cells(38). Similarly, TFG1 (Trk-fused gene 1), which interacts with Sec16A(39), forms a matrix at the interface between the ER and the ER-Golgi Intermediate Compartment (ERGIC) through oligomerization of C-terminal PQ (proline-glutamine)-rich IDRs (40,41)....