The interaction between photosystem I (PS I) and flavodoxin from the cyanobacterium Synechococcus sp. PCC 7002 was investigated by covalent cross-linking in the presence of a hydrophilic cross-linker, Nethyl-3-(3-diaminopropyl)carbodiimide. Under the experimental conditions employed, five distinct crosslinking products of flavodoxin and PS I subunits are formed. Immunoblot analyses show that these species are the result of cross-linking of flavodoxin to PsaC, PsaD, an unidentified low-molecular-mass PS I polypeptide, and a 15-kDa subunit. The latter has been indirectly identified as the PsaF subunit. Analysis of the interaction of flavodoxin with PS I from a psaE mutant indicates that the PsaE subunit is required for correct complex formation between flavodoxin and PS I, although this subunit is not directly crosslinked to flavodoxin. In addition, the cross-linking products of PsaD with PsaC and PsaL, and PsaE with PsaF, are observed. The covalent complex of flavodoxin and PS I is shown to be fully inhibited with respect to electron transfer to soluble flavodoxin, ferredoxin or ferredoxin :NADP+ oxidoreductase.