Despite significant progress in clarifying the subunit compositions and functions of the multiple NADPH dehydrogenase (NDH-1) complexes in cyanobacteria, the subunit maturation and assembly of their NDH-1 complexes are poorly understood. By transformation of wild-type cells with a transposon-tagged library, we isolated three mutants of Synechocystis sp. PCC 6803 defective in NDH-1-mediated cyclic electron transfer and unable to grow under high light conditions. All the mutants were tagged in the same slr1097 gene, encoding an unknown protein that shares significant homology with the Arabidopsis protein chlororespiratory reduction 6 (CRR6). The slr1097 product was localized in the cytoplasm and was required for efficient assembly of NDH-1 complexes. Analysis of the interaction of Slr1097 with 18 subunits of NDH-1 complexes using a yeast two-hybrid system indicated a strong interaction with NdhI but not with other Ndh subunits. Absence of Slr1097 resulted in a significant decrease of NdhI in the cytoplasm, but not of other Ndh subunits including NdhH, NdhK and NdhM; the decrease was more evident in the cytoplasm than in the thylakoid membranes. In the ∆slr1097 mutant, NdhH, NdhI, NdhK and NdhM were hardly detectable in the NDH-1M complex, whereas almost half the wild-type levels of these subunits were present in NDH-1L complex; similar results were observed in the NdhI-less mutant. These results suggest that Slr1097 is involved in the maturation of NdhI, and that assembly of the NDH-1M complex is strongly dependent on this factor. Maturation of NdhI appears not to be crucial to assembly of the NDH-1L complex.