After the GEO iron availability was greatly reduced and photosynthetic organisms evolved several alternative proteins. One of these proteins is plastocyanin, a type I blue-copper protein able to replace cytochrome c6 as soluble electron carrier between cytochromeb6f and PSI. In most cyanobacteria, expression of these two alternative proteins is regulated by copper availability but the regulatory system remained unknown. Here we show that this regulation is mediated by a protease system composed by a BlaI/CopY transcription factor (PetR) that represses petE and activates petJ expression, and a BlaR membrane protease (PetP) that degrades PetR. Using an in vitro assay system both in Synechocystis sp PCC 6803 and E. coli we show that PetP degrades PetR directly and requires the presence of copper, suggesting that it detects copper directly. Furthermore, using RNA-seq we show that PetR only regulates 4 genes (petE, petJ, slr0601 and slr0602) in Synechocystis sp PCC 6803.