During haem and chlorophyll biosynthesis, flavin-dependent protoporphyrinogen IX oxidase catalyses the six-electron oxidation of protoporphyrinogen IX to form protoporphyrin IX. In the following step, iron is inserted into protoporphyrin IX by ferrochelatase. Based on the solved crystal structures of these enzymes, an in silico model for a complex between these two enzymes was proposed to protect the highly photoreactive intermediate protoporphyrin IX. The existence of this complex was verified by two independent techniques. First, co-immunoprecipitation experiments using antibodies directed against recombinantly produced and purified Thermosynechococcus elongatus protoporphyrinogen IX oxidase and ferrochelatase demonstrated their physical interaction. Secondly, protein complex formation was visualized by in vivo immunogold labelling and electron microscopy with T. elongatus cells. Finally, oxygen-dependent coproporphyrinogen III oxidase, which catalyses the formation of protoporphyrinogen IX, was not found to be part of this complex when analysed with the same methodology.