The FtsH family of proteases are membrane-anchored, ATP-dependent, zinc metalloproteases. They are universally present in prokaryotes and the mitochondria and chloroplasts of eukaryotic cells. Most bacteria bear a single ftsH gene that produces hexameric homocomplexes with diverse house-keeping roles. However, in mitochondria, chloroplasts and cyanobacteria, multiple FtsH homologues form homo and heterocomplexes with specialised functions in maintaining photosynthesis and respiration. The diversification of FtsH homologues combined with selective pairing of FtsH isomers is a versatile strategy to enable functional adaptation. In this article we summarise recent progress in understanding the evolution, structure and function of FtsH proteases with a focus on the role of FtsH in photosynthesis and respiration.