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 made use of Y. lipolytica tagged mutants affected in the inactivation of peroxisomal enzymes under pexophagy conditions, Ain16 and Ain19. Both strains appeared to be disrupted at two different sites of the same gene, YlTRS85, the ortholog of Saccharomyces cerevisiae TRS85 that encodes 85 kDa subunit of transport protein particle (TRAPP). Y. lipolytica trs85 mutants had multiple defects of protein transport to external medium, cell wall and vacuoles, indicating that YlTrs85 is indeed the ScTrs85 functional homologue, required early in the classical secretory pathway. Interestingly, peroxisomes were not able to reach vacuoles under pexophagy conditions in both Ain16 and Ain19 strains. Therefore, the essential role of the early secretory flow in selective macroautophagy of peroxisomes is suggested.