The crystal structure of 8-HDF type photolyase from Anacystis nidulans showed the similarity of the backbone structure with MTHF type E. coli photolyase but completely different binding site of the light-harvesting cofactor. This is a first example that homologous primary and tertiary structures in closely related proteins recognize two different types of cofactors at different binding-sites. The structure and function of photolyase and its cofactor recoginition are reviewed and discussed.