The redox sensitive proteome in eukaryotes comprises proteins that can be modified in the presence of reactive oxygen species (ROS). Reversible oxidation of proteins by ROS constitutes an important redox signaling mechanism. Anecdotal evidence suggested that several redox sensitive proteins originated from the plastid ancestor. However, the major evolutionary transitions of redox signaling in eukaryotes remain unknown. Here we perform a large-scale phylogenomic reconstruction of the eukaryotic redox sensitive proteome. In our study we analyzed redox sensitive Cys residues in protein sequences of the diatom Phaeodactylum tricornutum. Our comparative analysis includes 132 genomes from which 7,326 phylogenetic trees are reconstructed. We find that the majority of redox sensitive Cys residues (52%) are encoded in genes with prokaryotic nearest neighbors in eubacteria. The remaining reactive Cys are encoded in eukaryotic specific genes (39%), genes with prokaryotic nearest neighbors in archaea (5%) or genes that could not be classified (4%). Evolutionary reconstruction of amino acid ancestral states reveals that redox sensitive Cys residues are 2-fold enriched in genes whose origin coincides with the primary plastid endosymbiosis event in comparison to the background Cys residues. Furthermore, we find a similar enrichment regarding amino acid replacements into redox sensitive Cys that coincides with the secondary endosymbiosis event. Our results reveal direct inheritance of redox sensitive proteins from the plastid ancestor by primary endosymbiosis as one major expansion of the redox proteome. This was followed by adaptation of existing genes to extended redox signaling linked to the secondary endosymbiosis event. Thus, the primary and secondary endosymbiosis events played a key role in the evolution of the redox sensitive proteome in eukaryotes, either via endosymbiotic gene transfer or by linking already existing proteins into the redox signaling network.