Clathrin-mediated trafficking is a conserved process during which clathrin coated vesicles transport cargo between the trans-Golgi Network (TGN) and the endosomes, and during the process of endocytosis. These studies identify a previously unrecognized sequence of assembly between adaptor-specific clathrin coated vesicles. At the TGN, we found that GGA-enriched vesicles form first, followed by the biogenesis of AP-1 enriched vesicles. We then identified the mechanism by which this process is temporally controlled. We have identified a novel direct physical interaction between the VHS domain of Gga2 and the yeast PI(4)-Kinase, Pik1p, that is important for the recruitment of Pik1p to the TGN membrane. Deletion of GGA proteins results in the delay of PI(4)P accumulation and Pik1p recruitment. Furthermore, we have mapped the regions through which Pik1p interacts with Gga2 and demonstrate that these binding sites are important for the Pik1p-GGA interaction in vivo. Disruption of these binding sites through mutation results in delayed PI(4)P accumulation, mislocalized Ent5p and delayed AP-1 recruitment. We also provide evidence that this Pik1/GGA interaction is regulated by GTP-Arf1. Arf1 binds to the GAT domain of GGA2, enabling Pik1p to directly bind to the VHS domain of Pik1p. We also find that this network of physical interactions is conserved in mammals.