© 2020 Hydrogen Energy Publications LLCPhotosynthetic purple non sulfur bacteria can be utilized in outdoor photobioreactors for sustainable large-scale biohydrogen production. However, the diurnal cycle under natural outdoor conditions affects hydrogen productivity and yield. Here, we investigated the effect of light and dark cycles on the hydrogen production metabolism of Rhodobacter capsulatus DSM1710 using custom-designed Affymetrix Gene Chip technology. R. capsulatus was grown by cyclic illumination on hydrogen producing medium. After three cycles of growth, the comparative transcriptome analysis of the light-period samples versus dark-period samples was carried out. The number of genes showing significant expression change was 914 out of 4052 probe sets in total. The differentially expressed genes were classified into metabolic groups. Genes related to nitrogen metabolism, photosynthesis, electron transport, transporters and central metabolism were up-regulated. In contrast, genes related to protein fate and stress metabolism were down-regulated. These gene expression results provide insight on the influence of the relevant metabolic pathways on hydrogen production under cyclic illumination.