The phylogenetic analysis of the rat and yeast peroxisomal proteomes reveals that the largest fraction of peroxisomal proteins originated within the eukaryotic lineage and that the significant fraction of peroxisomal proteins which stems from the alpha-proteobacteria is likely the result of a secondary retargeting from the mitochondrion. The most widespread and ancient set of peroxisomal proteins is mainly composed of eukaryotic proteins involved in peroxisome biogenesis and organization. Most of these core proteins are evolutionarily related to the Endoplasmic Reticulum Assisted Decay pathway, suggesting an evolutionary origin of the peroxisomes from the endomembrane system. While this manuscript was under review a common evolutionary origin of the Peroxisome and the ER was also proposed by Schluter and coworkers  based on the homologies in Figure 2 between ERAD and Pex proteins (Figure 2) while this homology has also been observed by Erdman and Schliebs . In the former analysis, full length homologs with Bacterial proteins were not included and the authors could not exclude that such proteins were indeed donated by an early symbiont. The retargeting of enzymes documented in this paper solves the paradox of a eukaryotic organelle with bacterial enzymes. Recent experimental work indicates that some peroxisomal proteins first enter the ER thereby capturing part of the ER membrane for subsequent formation of the organelle . These observations are consistent with our findings that the oldest PEX proteins are homologous to proteins of the ERAD pathway, suggesting that evolutionarily as well as ontogenetically peroxisomes are in fact offshoots from the ER.