Background: Epsilon-protein kinase C (εPKC) protects the heart from ischemic injury. However, the mechanism(s) of εPKC cardioprotection is still unclear. Identification of the εPKC targets may aid in elucidating the εPKC-mediated cardioprotective mechanisms. Previous studies, using εPKC transgenic mice and difference in gel electrophoresis, identified proteins involved in glucose metabolism, the expression of which was modified by εPKC. Those studies were accompanied by metabolomic analysis, suggesting that increased glucose oxidation may be responsible for the cardioprotective effect of εPKC. Whether these εPKC-mediated alterations were because of differences in protein expression or phosphorylation was not determined. Methods and Results: In the present study, we used an εPKC -specific activator peptide, ψεRACK, combined with phosphoproteomics, to find εPKC targets, and identified that the proteins whose phosphorylation was altered by selective activation of εPKC were mostly mitochondrial proteins. Analysis of the mitochondrial phosphoproteome led to the identification of 55 spots, corresponding to 37 individual proteins, exclusively phosphorylated, in the presence of ψεRACK. The majority of the proteins identified were involved in glucose and lipid metabolism, components of the respiratory chain as well as mitochondrial heat shock proteins. Conclusions: The protective effect of εPKC during ischemia involves phosphorylation of several mitochondrial proteins involved in glucose and lipid metabolism and oxidative phosphorylation. Regulation of these metabolic pathways by εPKC phosphorylation may lead to εPKC-mediated cardioprotection induced by ψεRACK. (Circ J 2012; 76: 1476-1485)