The degradation of organelles by autophagy is essential for cellular homeostasis. The Golgi apparatus has recently been demonstrated to be degraded by autophagy, but little is known about how the Golgi is recognized by the forming autophagosome. In this study, we performed a proteomic analysis of Atg5-deficient mouse tissues, and found that Golgi-resident transmembrane proteins YIPF3 and YIPF4 accumulated in the autophagy-deficient tissues. We developed two Golgiphagy-reporter systems and demonstrated that the YIPF3–YIPF4 complex functions as a Golgiphagy receptor. YIPF3 contains the core LIR motif and putative phosphorylation sites upstream of the LIR, both of which are required for the interaction with ATG8 family proteins. YIPF4 is also required for Golgiphagy, at least for stabilizing the YIPF3–YIPF4 complex. Interestingly, the sequence of the phosphorylation sites is exactly the same as that of TEX264, the major ER-phagy receptor, implying that a similar regulatory mechanism might exist.