Prokaryotic (6-4) photolyases branch at the base of the evolution of cryptochromes and photolyases. Prototypical members contain an iron-sulphur cluster which was lost in the evolution of the other groups. In the Agrobacterium (6-4) photolyase PhrB， the repair of DNA lesions containing UV-induced (6-4) pyrimidine dimers is stimulated by Mg . We propose that Mg is required for efficient lesion binding and for charge stabilization after electron transfer from the FADH chromophore to the DNA lesion. Furthermore， two highly conserved Asp residues close to the DNA-binding site are essential for the effect of Mg . Simulations show that two Mg bind to the region around these residues. On the other hand， DNA repair by eukaryotic (6-4) photolyases is not increased by Mg . In these photolyases， structurally overlapping regions contain no Asp but positively charged Lys or Arg. During the evolution of photolyases， the role of Mg in charge stabilization and enhancement of DNA binding was therefore taken over by a postiviely charged amino acid. Besides PhrB， another prokaryotic (6-4) photolyase from the marine cyanobacterium Prochlorococcus marinus， PromaPL， which contains no iron-sulphur cluster， was also investigated. This photolyase is stimulated by Mg as well. The evolutionary loss of the iron-sulphur cluster due to limiting iron concentrations can occur in a marine environment as a result of iron deprivation. However， the evolutionary replacement of Mg by a positively charged amino acid is unlikely to occur in a marine environment because the concentration of divalent cations in seawater is always sufficient. We therefore assume that this transition could have occurred in a freshwater environment.