Yarrowia lipolytica was recently introduced as a new model organism to study peroxisome degradation in yeasts. Transfer of Y. lipolytica cells from oleate/ethylamine to glucose/ammonium chloride medium leads to selective macroautophagy of peroxisomes. To decipher the molecular mechanisms of macropexophagy we isolated mutants of Y. lipolytica defective in the inactivation of peroxisomal enzymes under pexophagy conditions. Through this analysis we identified the gene YlTRS85, the ortholog of Saccharomyces cerevisiae TRS85 that encodes the 85 kDa subunit of transport protein particle (TRAPP). A parallel genetic screen in S. cerevisiae also identified the trs85 mutant. Here, we report that Trs85 is required for nonspecific autophagy, pexophagy and the cytoplasm to vacuole targeting pathway in both yeasts.