We demonstrated that a yeast deletion mutant in IPT1 and SKN1, encoding proteins involved in the biosynthesis of mannosyldiinositolphosphoryl ceramides, is characterized by increased autophagy and DNA fragmentation upon nitrogen (N) starvation as compared with the single deletion mutants or wild type (WT). Apoptotic features were not significantly different between single and double deletion mutants upon N starvation, pointing to increased autophagy in the double Deltaipt1 Deltaskn1 deletion mutant independent of apoptosis. We observed increased basal levels of phytosphingosine in membranes of the double Deltaipt1 Deltaskn1 deletion mutant as compared with the single deletion mutants or WT. These data point to a negative regulation of autophagy by both Ipt1 and Skn1 in yeast, with a putative involvement of phytosphingosine in this process.