Previously, we discovered that Arl1 and Ypt6, the two small GTP-binding proteins that regulate late Golgi vesicle traffic, also have roles in autophagy (Yang and Rosenwald 2016). Interestingly, we discovered that a simple knockout of one of the two genes did not impair autophagy at 30°, yet both arl1Δ and ypt6Δ strains showed completely defective autophagy at 37°. Furthermore, we found that Arl1 and Ypt6 participate in autophagy through interactions with the GARP complex. Retention of both Arl1 and Ypt6 is required for the proper localization of the GARP complex to the PAS at 37°, and thus affects membrane transport from the TGN to the PAS for autophagosome formation. An absence of one of the two is apparently no longer sufficient to securely bind GARP to the PAS at high temperature. Because the autophagy pathway is very complicated, we sought to identify other regulators that work cooperatively with Arl1 or Ypt6 to affect autophagy under high temperature stress.