Purple non-sulphur phototrophic bacteria (PNSB) are excellent models for analysing the co-ordination of major metabolisms, including oxidative phosphorylation, photophosphorylation, carbon dioxide fixation and nitrogen fixation. In species studied to date, a two-component system called RegBA controls these functions and it has been thought that this redox sensing regulatory system is essential for co-ordinating electron flow and cannot be easily replaced. Here we show that this is not the case for all PNSB and that the oxygen-sensing FixLJ-K system, initially described in rhizobia, controls microaerobic respiration, photophosphorylation and other major metabolic traits in Rhodopseudomonas palustris. A R. palustris fixK mutant grew normally aerobically but was impaired in microaerobic growth. It was also severely impaired in photosynthetic growth. Transcriptome analyses indicated that FixK positively regulates haem and bacteriochlorophyll biosynthesis, cbb3 oxidase and NADH dehydrogenase genes, as well as genes for autotrophy and aromatic compound degradation. Purified FixK interacted with the promoters of a bacteriochlorophyll biosynthesis operon, a bacteriophytochrome-histidine kinase gene and the fnr-type regulatory gene, aadR. A FixK-AadR hierarchy mediates the transition from microaerobic to anaerobic growth. These results underscore that physiologically similar bacteria can use very different regulatory strategies to control common major metabolisms.